I'm sure they'd be allowed to cross categories if they did a live action episode.
The Academy's statement makes it sound like that wouldn't even be necessary.
' However, if an animated series opts to enter in Comedy Series rather than Animated Program category, then the individual achievement categories are open to them, e.g., writers can enter Writing for a Comedy Series category. '
So apparently they have the option of competing against every other show on TV instead of just other animated shows, they just choose not to.