It's pretty easy to litter train a bunny. They do intentionally leave territorial poops anyway, but those are hard little balls at the edges and corners of the room, so not too obnoxious.

The most difficult thing about a free roaming bunny is that the like to chew (it's more correct to say they have to chew, since their teeth always grow), and getting them to chew what you want them to chew, not what you don't want, is a challenge.