why didn't they just make humanoids?
It does appear logical to me, sort of. These Progenitor folks supposedly began their galactic seeding program because they felt their own mortality catching up on them. They were lonely, they knew they'd go extinct one day, they wanted to leave a monument in form of some sort of offspring, and they didn't want this offspring to be as lonely as they had been.
Yet the offspring would also be mortal and eventually go extinct. So in order to keep the galaxy populated with the desired "humanoid monument", the Progenitors would have to program a succession of emergencies: a couple of thousand humanoid species emerge first, meet each other, perhaps fall in culturo-technological synch, vie for supremacy, and ultimately go extinct - and then a next batch emerges from previously humanoid-free biospheres and does the same.
The Progenitors began their program five billion
years ago. There could have been quite a few cycles of humanoid cultures there, if a typical culture normally goes from humanoid through techno-humanoid to noncorporeal in a matter of tens of millennia at most...
No doubt the project would go astray at some point. But it makes sense that it would begin in an orderly fashion, with several dozens or hundreds of cycles of humanoids sticking to the original parameters - because the Progenitors programmed those parameters to be simple and universal, with few bells and whistles and very little in the way of variation. That the various species in the Trek 24th century are compatible is only a sign of good engineering - in the 24,000th century, the differences will probably be somewhat more severe, and the monument will start to crumble.