I think there's definitely a lot of "but Twilight is JUST LIKE US so she CAN'T be a princess because that would mean that SHE'S NOT LIKE US ANYMORE!!!!"-type projection going on.

But I don't think that any Bronies are pretending that Twilight isn't a girl...? I mean, she's already a purple unicorn named Twilight Sparkle who fights evil with a magical tiara and who is given a very, very feminine voice by Tara Strong. I think a lot of Bronies identify with her because she's antisocial and nerdy, but I don't think that they view her as "not feminine" in any way. At least not the way that you're describing being able to view Kid Icarus as "not masculine" and therefore being able project femininity on him because he looked like a girl. Twilight Sparkle doesn't look like a boy or sound like a boy, so it's not quite the same thing.

But yeah you're definitely right that SOME element of projection is clearly at work here, and Twilight becoming a princess messes with that projection/identification because Bronies don't want to identify with a character who is a princess. Because princesses are icky. Or something.