I think that might depend on the individual, so I'd wait for official word from
@Crow about that one. I'm playing it that everyone's taking for granted they're in a crossover setting and thus my characters aren't likely to comment on it. Here, they're all students at the high school, regardless of whatever else they may be, and that's that. If one wanted to play up some genre savvy or similar and actively comment on things being unusual, that is also perfectly fine, of course. My guys wouldn't actively call attention to the fact that they're in a crossover setting, although they probably still could comment on someone being a magical girl, etc. They just wouldn't in any way imply that said someone must be from her own magical girl anime series, because that's impossible. So my view on it is, in the setting of the RP, we're all in/from the same setting. We just also happen to all belong to our own individual series. If you've ever seen the Super Robot Wars games, it'd be something like that: Mazinger, Getter Robo, and Gundam are completely independent, but in the game they're all in the same setting and take it all in stride as such.
Runa being a naive idiot means she's even more likely to not question things and just assume everyone is how they is without further comment, but that's a separate matter. I guess another way to think of it is, say, we could all comment that there's some crazy civil war going on on Jura, or there's mecha fighting aliens from the moon, for example, because we're in a unified setting. It's a weird take, and just my opinion on how to treat things.
...I guess what I'm getting at is that Jonathan's comment is a valid one, but stated as a hypotehtical. Everyone's both from another independent setting, AND just in this unified one, or something. I'm rambling, I'll stop now.