Something I've noticed is that the mods at TV Tropes seem to think that only good guys can have blue and orange morality. Why is that? What is keeping them from believing that a straight-up villain can have blue and orange morality?

Blue and Orange Morality is a strike against evilness as they are less capable of realizing their wrongdoing. BOM trends more to neutral alignments than good or evil.

But it's not a disqualifier as many villains, even approved Complete Monsters, have this trope if they do enough evildoing it's no longer enough to mitigate.

I disagree: BOM doesn't mean good or evil isn't there; it's just incomprehensible to us how they got there. In many cases it may show neutrality, but that's by no means a certainty.

So, no, BOM isn't an alien barometer of good or evil any more than smelling the color 9 is. It's incomprehensibility, pure and simple, and the results are what you end up judging.

You know, just like in real life, when people do the right things for the wrong reasons and vice versa.