The extraterrestrial seeding theories are all a bit suspect to me from a scientific point of view (besides the Adam and Even nonsense from Return to Tomorrow).
We already know that modern humans descended from primates which have been on earth for 65 million years, and their evolutionary roots can be traced back to the common ancestor of all mammals, the Synapsids, which lived 250 to 300 million years ago. So any exogenic explanation for the origin of humanity has to be set much earlier than half a million years ago. And the "seeds" themselves would have had to been single-celled organisms to explain what we know from modern genetic analysis of life on Earth.
A more plausible explanation is one that attempts to explain why so many species on different alien worlds have near-identical analogs on Earth (hawks, dogs, lizards, beatles, worms, etc.), and that would be convergent evolution.
It's possible that due to similar environments existing on different worlds, evolution has independently found the same "solutions" in terms of general body layout and organ function. Physics (for the most part) follows the same rules no matter what planet you're on, so that in itself is going to eliminate certain body designs while gravitating towards others.
That would explain why most complex life forms are bilateral-symmetric and only a few are radial-symmetric. It also explains why most animals have an even-number of limbs and heads are placed at the front or top of the body.
So the reason why humanoid species are so common in Star Trek is probably because the humanoid body shape is the natural upright evolution from a quadriped bodyshape, and it's one that allows one to use their hands for manipulating the environment (e.g. creating and using tools). And we don't see any sapient aliens with 2-mouths or eyes on their back because it's just inefficient to have these designs.