As far as I know, the 'ancient race that created everyone else' has never been mentioned in Star Trek again (at least on TV) and I hope it stays that way. Let that episode die in the memory hole.

The genetic engineering ban always rubbed me the wrong way. Like... these people claim to as Picard put it, have "more evolved sensibilities" or whatever where revenge, greed and racism are a thing of the past and time and time again we see that the federation basically baked racism into their laws. The way Bashir and Una were treated after it was found out they had been genetically altered says everything. It wasn't even Bashir's decision and the federation went after him. Genetic alteration was part of Una's culture and she was roasted for that despite the federation claiming to be tolerant of other cultures... until theyre not. Theres an entire episode about what happened when Una's people removed these alterations just to die for it. Or turn into techno ghosts idk. And Pike basically says the quiet part out loud more or less saying he tolerates her because she is "one of the good ones." Which is what a lot of racists do. They'll dismiss entire ethnic groups then turn around and say "oh no not you, you're one of the good ones. Its all the other dirty (insert ethnic slur here) that are the problem.

I get what the rationalization for the ban is but in reality it is racism. It is racism that is rationalized because of bad prior experiences like much of racism is. i.e people looking for reasons to hate, exclude and persecute entire groups of people. "I was jumped in an alley by someone of (insert ethnicity here) and therefore all members of that ethnicity are violent is a logical fallacy as the entire argument just like the federation being dicks to anyone that was genetically altered because of what Khan did.

They also had The Paradise Syndrome where a race of progenitor aliens were putting humans on other planets. Just saying that they discovered that those aliens also modified humans to best survive on whatever planet they resettled them would have solved the problem.

It's also not even remotely how DNA or evolution work.

I think humanoid is a perfectly logical end-state for any terrestrial species that develops technology:

Gotta get energy somehow, consumption is more energy dense than autotrophy, so need a mouth. Gotta find the stuff to put in mouth, so need sense organs, closer to mouth is better. Light is generally the best medium for sensing, so eyes eventually. Two eyes are way better than one for depth perception, but three is inefficient energy investment with seriously diminishing returns.

Gotta move around in a gravity well to get to your food, so you need some kind of limbs. In the beginning, before developing the sophisticated nervous system necessary for dynamic locomotion, four is the minimum so you can remain stable on three limbs while you move the fourth.

Gotta start banging rocks together if you want tech, so you need hands of some kind, and two free limbs. By this point, your nervous system should be sophisticated enough to allow dynamic locomotion, but you still need at least two "legs" to move relative to each other to move on the ground in a gravity well.

I would expect most technological species with similar heritage to humans to look roughly humanoid. There are plenty of other forms, but I feel like they'd be selected against.

I have no clue why the Klingon thought a superweapon would be hidden in the DNA of multiple species as a puzzle.

But then the puzzle idea makes no sense, so why the hell not?

But why even make the puzzle to begin with?

And it doesn't really explain why everyone looks humanoid because their life seeding started at a much earlier stage and just apparently hoped evolution would do the rest of the work. You can't start with an amoeba and expect it to evolve into something that looks like a human but may or may not have ridges or spots on their head. That's ludicrous.

So it was all a ruse?

No, it works like attorneys general. Jeffrey's Combs

I think Combs is Welsh, so it's Combson if I'm not mistaken