I think (hope) things will improve with time. At the moment, Bertie will still have residual hormones in his body. So that will contribute to his behaviour (spraying) and hers (territorial). It’s also not unusual for rabbits to have “poop wars” when bonded and newly bonded. So I can only advise just keeping on top of the mess, putting everything back in the litter boxes and waiting this out. The extra boxes are certainly a good idea. Hopefully you will be able to scale back on those eventually. I remember a member here a few years ago had the rabbit pen pretty much all litterboxes. She graduallly reduced the number. So that’s another idea…
A large litterbox that easily fits them both with room to spare is a good idea also. Sometimes you’ll get a rabbit in a smaller litterbox and the other rabbit decides to sit outside of it, toileting. Even though there are other boxes available to them. They want the one that is occupied and will mark next to it if they cannot access it.
I would use a larger one for their permanent litterbox after the habits have improved.
With my bonded pairs, they always remained a bit messier then they were as single rabbits. That’s not true for everyone though. Mine do pee in the boxes though and most poop goes there. There is just some scattered poops also to deal with.