In Armageddon, Onaga is inhabiting his original body instead of possessing Reptile. That's what he always looks like.
Raiden's MKDA ending is just an early, noncanon design, like concept art. And he didn't look human in it.
Here's the highest def version of the picture I could find, see for yourself:

That's kind of what I thought, but I wasn't sure. I figured that pic was just an early design, before Midway decided to make him the boss of Deception and really flesh out his reptilian look. You can tell in that pic he isn't human, but still has a humanoid look if you know what I mean. The canon Reptile ending always had me curious though. Thanks Razor.

Onaga's MKDA design must be a very early one,so they decided to change it in Deception.

I reeally don ́t know but good question.