Relative to interbreeding of the sub-species on Star Trek, the underlying premise is that all those sub-species had a common origin that is unknown, i.e. an advanced civilization that spread through the universe and then vanished but leaving their genetic heritage in the universe. Thus is the ability for them to interbred.
The plot of the TNG episode “The Chase”. A billion years is more than enough time for speciation to occur, however. “Humanoids” would look nothing alike after only a few million years, let alone be able to breed.