Roddenberry
I think you guys are thinking too hard. The real reason all the aliens in Star Trek look like people with Silly Putty stuck to various parts of their faces is because it's cheaper to film than building real aliens. Toward later years this improved a bit as computer animation got cheaper, but it's hard to do Real Aliens cheap.
All the Progenitor stuff is just fluff to try and explain it.
I have no doubt that if Roddenberry had the ability to people his universe with unearthly creatures on his cheesy budget, he would have.
Some fairly decent Real Aliens can be seen on Farscape and Babylon 5, although most of the aliens are still people in makeup.