whether the fact they are aliens is central to the plot or they are already long established on earth so that it really means nothing other than a quick throwaway line about them being martial artists from another galaxy who just happen to resemble bipedal turtles doesn't really matter
what matters is that they are going to be alien.
Big part of the plot or small part of the plot it is all the same and what both these options are is.... LLLLLLLLLLAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMEEEEEEE EEEEEe
Turtles are mutants not aliens.
Hell I could buy an alien influence if they say it was an alien mutagenic ooze that turns four ordinary turtles and a rat into kick ass martial artist fighting machines but making them actually aliens
this is for Bay and whoever the heck is writing this movie