You can't really apply real-life scientific concepts to Star Trek in this area. Even with the "explanation", it makes absolutely no sense. Klingons, Humans, Vulcans, Cardassians, etc. regularly interbreed, which essentially makes them the same species, despite having evolved on different worlds. How could that possibly happen, even with transplanted DNA code segments (TNG: The Chase), when mutations are random?
And how could so many intelligent alien species have evolved to look exactly like humans, except for having funny ears, bumpy foreheads and weird skin conditions?
I don't take that very seriously, in the original star trek, even the kllingons were human looking, and even though that was pathetically explained as something shameful, in reality it's just due to budget limitations.
However don't forget that one episode where an ancient civilization seeded life all over the galaxy.. so should it be so far fetched that a great number of civilizations would be so similar to humans, if they all had a common ancestory?