It sounds like you need to place litter boxes in the more open area. You can think that a rabbit doesn’t truly understand the somewhat arbitrary rule we’re enforcing that they should only go to the bathroom in a singular spot. Rabbits aren’t actually litter-boxed trained per-say— it’s more that their natural bathroom habits fits the litter-box model well. So there are still many circumstances where negotiation is needed, like re-arrangement, additional litter boxes, walling off places (ex. beds, couches…).
Re: the reaction to the restricted play area, that also makes sense to me. Marking the border, in my experience with a neutered male who is not very adherent, tends to communicate, “Hey I want to go past here”, “Hey I’m bothered I can’t go past here”, or something along those lines. I think there is some defiance to it. You can try some things to reduce it, like cover the wall so it seems solid and doesn’t seem like there’s something past there. You can put objects in those hot spot areas so it’s less welcoming to peeing as well. Establishing a signal can also be helpful, especially since your rabbit seems to already pick up what you approaching means. I use a short, loud snake “hiss” sound when I see my neutered male about to go where he shouldn’t, and that usually either jolts him to a litter box or pauses him enough for me to get to him and coax him to the closest box.
The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.