If said fantasy video game is going to use scientific evolutionary theory to justify a race's existence, then yes, they should abide by a basic understanding of it. That's what makes fantasy believable; the things we believe in should be able to stand up to scrutiny. Both in the fantasy...
It's just another case of Nintendo not understanding science, like Zelda being forced to eternally give birth to herself via the "unbroken Hylia bloodline". A way of trying to "explain" an appearance of a new race in the series when all they could've said was that the Rito were there all along...