Rabbits can change their inclinations as they get more used to the environment. I am not a rabbit mind reader, but I imagine it’s like when you have a revelation of “wait, was that hallway always there?”, where the rabbit suddenly perceives that they can do something outside their routine to make their life easier. In this example, it’s easier just to poop right there, then hop over to the litter box. As kurotta mentions, rabbits like doing those things all at once.
It’s good that you’re being conscientious of keeping routine, but a think rearranging the bowls won’t be too traumatic. Plus it’s a health hazard for that material to be around eating/drinking stations. Wick will sometimes kick a poop in his water bowl, and you can imagine how bad that could get for festering bad bacteria and attracting bugs!
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.