The combine are aliens from space

Actually, technically, the way teleportation works in Half Life/Portal universe...

They are aliens, extraterrestrials, they're not from ... a mirror realm, a distinct and different universe or timeline.

Xen acts as a kind of ... bus stop, for the universe, if that makes any sense. But it does exist somewhere in our Universe, it is not in an alternate/parrelel universe/timeline ala Marvel different universes.

Xen is a relay, that, for whatever reason, seems to be a spot in the actual universe where transdimensional travel often ... ends up at, or traverses through. Like a strange attractor in a chaotic system.

So this goes for the Combine as well. Xen, Vorts, Headcrabs, the Combine... they are all from our Universe, though they could be from totally different galaxies than our own.

The teleportation tech/system in the HL/Portal Universe works more like the Webway from 40k, than it is like the Warp from 40k.

It is a system / series of gateways in ... string theoretic 11 dimensional space, that in our 3d experience of reality, appear as basically a complex network of subway tunnels, semi-stable wormholes. The Combine make great use of this, the Human Resitance barely understand it, but use it in different ways, and the Portal tech just most directly punches wormholes through 3d space via ... fucking moondust and intensely technogically perfected spite, or something.

... even in the instances in the series where time itself is ... paused or traversed... by G Man or the Vorts ... these occurences seem to all take place inside of a single consistent and coherent universe.

Alien just means from somewhere other than earth. Another dimension pretty much fits the bill, there. Like, you're simultaneously being too and not enough pedantic for your argument to really hit. The uncanny valley of pedantry