I have two Flemmies, a girl and a boy, both about 18 weeks old, both just been neutered.
The girl is wonderfully toilet trained, even before the spay, she’s so neat and tidy, only occasionally will I find a little pooh not in her litter box. Unless the box is too full, then she poohs and pees very close to it – doesn’t like getting her paws dirty!
The boy, on the other hand, sprayed and poohed as he bounced before the neutering. Afterwards the spraying stopped and he started collecting his poohs and wees in two places in his area. In his cage he was quite tidy, but outside of his cage he poohed/wees in a very large area, but the same general area. So an improvement, but nowhere as good as the girl.
Now I’m reintroducing the two bunnies, and the boy is making a mess everywhere again, but no spraying. I think it’s a territorial thing, and that it will improve.
So partly it could be personality, or it could be gender.
Confining them to a small space certainly seems to make them be tidier, otherwise they are always stepping in their own pooh.