Ugh, that episode is so fucking stupid. "We wanted to pass information down to our creations, but we hid it in a puzzle for no apparent reason and just hoped that all the pieces of the puzzle would evolve into spacefaring civilizations that will all work together to solve the puzzle." And that didn't even happen because one of the pieces was on a world which didn't have much life on it and it got intentionally destroyed during the race for all the puzzle pieces.
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.
They wanted to explain why there were so many accidental alien-human hybrids. Because someone forgot that Spock was originally described as being a product of medical science.
Which should have been the answer to every hybrid, their parents made a deliberate choice to have a child, and then did some genetic engineering to get it done.
But the writers wanted to inject drama with accidental hybrids. Also they decided that genetic engineering was banned so that Khan could be an enemy. A good choice because that movie was great. But a bad choice as well because it led to this episode.
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.
I didn't care for it either. It was like they wanted to explain why every alien race looked like humans in costumes, but I was perfectly fine with suspension of disbelief.
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.