The Naassenes are documented in Hippolytus's Refutations volume 5, and one of their primary religious texts was the Gospel of Thomas.

Before digging into those texts themselves, it's also important to know the philosophical context in which they arise, specifically the debate between Epicurean material naturalism and Plato's theory of forms vs images.

The TLDR on the background is that the Epicureans rejected intelligent design and claimed life evolved through natural processes, and Plato claimed there was a spiritual perfect form with a lesser physical incarnation (and then there could be images of physical things like an artist illustrating a physical bed that was modeled from the spiritual form of a bed in Republic book X).

You see this topic discussed early on in Christian circles in Paul's first letter to the Corinthians, which touched on certain ideas later found among the Naassenes like the dual Adams:

It is sown a physical body; it is raised a spiritual body. If there is a physical body, there is also a spiritual body. Thus it is written, “The first man, Adam, became a living being”; the last Adam became a life-giving spirit. But it is not the spiritual that is first but the physical and then the spiritual.

• 1 Cor 15:44-46

So starting with the Gospel of Thomas, you have:

Jesus saw some babies nursing. He said to his disciples, "These nursing babies are like those who enter the (Father's) kingdom."

They said to him, "Then shall we enter the (Father's) kingdom as babies?"

Jesus said to them, "When you make the two into one, and when you make the inner like the outer and the outer like the inner, and the upper like the lower, and when you make male and female into a single one, so that the male will not be male nor the female be female, when you make eyes in place of an eye, a hand in place of a hand, a foot in place of a foot, an image in place of an image, then you will enter [the kingdom]."

• Thomas 22 (worth nothing that the Coptic here explicitly used the same Greek term for images as Plato used)

Later on, in describing its creator figure, it expounds:

Jesus said, "If they say to you, 'Where have you come from?' say to them, 'We have come from the light, from the place where the light came into being by itself, established [itself], and appeared in their image.'

If they say to you, 'Is it you?' say, 'We are its children, and we are the chosen of the living Father.'

If they ask you, 'What is the evidence of your Father in you?' say to them, 'It is motion and rest.'"

His disciples said to him, "When will the rest for the dead take place, and when will the new world come?"

He said to them, "What you are looking forward to has come, but you don't know it."

• Thomas 50-51 (again, it's worth remembering that the transition from physical to spiritual embodiment was supposed to happen when the new world arrived per Paul's letter, so the over-realized eschatology here indicates spiritual embodiment)

There's an additional indicator in Thomas is here:

Jesus said, "Images are visible to people, but the light within them is hidden in the image of the Father's light. He will be disclosed, but his image is hidden by his light."

Jesus said, "When you see your likeness, you are happy. But when you see your images that came into being before you and that neither die nor become visible, how much you will have to bear!"

• Thomas 83-84

The challenge with discerning the earlier ideas of the Naassenes in Pseudo-Hippolytus is twofold - one, it is written by the opposition, and two, this is after Gnostic circles were heavily influenced by Neoplatonism which flipped the script back from "physical first then spiritual" (as Paul cited) to Plato's spiritual first then physical (which belies the earlier use of images in Thomas as Plato's images only followed physical incarnation and it was form that preceded the physical - a term absent in Thomas).

Yet still you have indications breaking through in Refutations for the Naassenes:

They rashly assume in this manner, that whatsoever things have been said and done by all men, (may be made to harmonize) with their own particular mental view, alleging that all things become spiritual. [...]

And the aforesaid images are figures of the primal man, and of that spiritual one that is born again, in every respect of the same substance with that man. [...]

We, however, he says, are spiritual [...]

That which is, he says, nothing, and which consists of nothing, inasmuch as it is indivisible — (I mean) a point — will become through its own reflective power a certain incomprehensible magnitude. This, he says, is the kingdom of heaven, the grain of mustard seed, the point which is indivisible in the body; and, he says, no one knows this (point) save the spiritual only.

• Hippolytus's Refutations V

Looked at through the lens of canonical Christianity, these ideas say one thing, but through the lens of Thomas (the group in question is the only one explicitly said to have been following it) the interpretation is wildly different.

In Thomas, the cosmos is already a dead body (like Leucretius's claims the cosmos was like a body that would one day die). The rest for the dead and the world to come has already happened but we don't realize it. The images around us are its creator's light, a creator that was eventually established in light and took on earlier images. Adam (which can be translated as humanity) came from great wealth but is now dead, and we are allegedly the children of its eventual creator of light (which in Pseudo-Hippolytus is clearly described as having been brought forth by an original Primal Man/humanity).

Also important is that contrary to the canonical interpretation of being born again, in Thomas being born again is literally being born as babes, with "a hand in place of a hand" and "an image in place of an image."

The key component here is the foundation of Epicurean naturalism. That's very present in Thomas, which entertained naturalism as the origin of the soul (saying 29) but lamented and rejected the Epicurean claims of the soul's dependence on the body (saying 87), appealing to an eventual demiurge in line with Plato's ideas as recreating the images of what came before in its light.

By the 4th century when Pseudo-Hippolytus is recording the beliefs, Epicureanism has fallen from favor in the rise of Neoplatonism which muddies the waters a fair bit, and yet you still have repeated claims of its audience actually being spiritual as well as the quite radical idea that its creator was brought forth by an earlier 'man.'

An important context for why these beliefs might have been deemed necessary can be seen in Against Heresies book 2 chapter 14 discussing 'Gnostic' beliefs in the 2nd century in general:

Then again, as to the opinion that everything of necessity passes away to those things out of which they maintain it was also formed, and that God is the slave of this necessity, so that He cannot impart immortality to what is mortal, or bestow incorruption on what is corruptible

If there are limits on divine powers such that what is mortal cannot be immortal, then immortality can only be achieved by being born immortal. Hence the development of beliefs of a second birth from mortal form to immortal. Which in Thomas differs from canonical tradition in that it is not a symbolic ritual but literal birth as a babe, much as its Eucharist is not of consuming a physical body but in consuming the words left behind (saying 108).

If you are interested in this topic, I can't recommend enough reading through De Rerum Natura first. The Naassenes explicitly describe the origin of the world as owed to indivisible points called seeds, language that is uniquely from Leucretius who writing in Latin used 'seed' in place of the Greek atomos. To say nothing for the close parallels between Thomas and the work regarding cosmos as dead bodies or referring to seed falling by the wayside of the path (in Leucretius describing failed biological reproduction and in Thomas describing what survived to reproduce as what multiples following a saying about how the human being is like a big fish selected from smaller ones).

There's no reason to believe that the second round of science would still arrive at earlier theories such as the pudding model of the atom.

That was very much a part of science. But it isn't any longer as a result of experimental evidence.

So your rebuttal glosses over the many failed scientific theories but then uses the failed religious ideas to invalidate any religious ideas.

When in truth, both science and religion have historically attempted to explain the unexplained. The methodology of science is much better, but they have both had many examples of dumb ideas in retrospect.

The reason why the Naassenes had such interesting ideas was that they ended up having incorporated the ideas of Leucretius, who in 50 BCE had written the only extant work from antiquity to describe survival of the fittest in detail.

At the time, there was no experimental evidence to support or falsify such theories. But at the time a religious group working on extrapolating theories built on top of naturalism ended up landing on very similar ideas to what we currently come up with having experimentally landed on evolutionary theory and having turned Plato's eventual creator of worlds (another philosophical influence on the Naassenes) from theory to practice.

So while science is more likely to be right more often as a result of far better methodology, the problem with the quote is that it's a "heuristic that almost always works" and fails to consider the edge cases when religious thought had attached itself to natural explanations which later turned out to be correct.

Effectively, any ideas predicated on concepts which will eventually be experimentally validated should be expected to arise again even after erasing earlier theorizing, as it's the replicability of experimental results that drives that reproduction. And any ideas, whether a part of science or outside of it, which are predicated on eventually falsified ideas have no guarantee of reproduction.

The mistake the quote embodies is the assumption that it's impossible for theological ideas to have attached themselves to experimentally reproducible concepts. But that has happened before, and it meant that the extrapolated theological concepts were also reproduced.

And that's to say nothing for the many reproduced beliefs on other reproducible foundations such as dying and rising gods or katabasis that occurred in completely separate communities. In those cases it was a result of watching the stars and observing the orbit of Venus dropping down below the ground to arise again days later. So you had a central American God navigating the underworld and resurrecting the dead associated with Venus independent and parallel to Ianna in the Mediterranean navigating the underworld and associated with Venus. Or the common beliefs about the immortality of snakes because of their shedding.

The quote is the kind of thing that seems clever but is factually incorrect and betrays the one offering it up as uninformed of what they are talking about despite their self-assuredness in borrowed pithiness.