A reaction by JV's Galactic Adventures puts into perspective why Wallace was gaining weight in the first place. Not because he was getting older and not just because he was eating lots of cheese, but mostly because his automated lifestyle meant Wallace wasn't exercising enough. He doesn't even use the stairs to come down. If anything, his weight gain is a natural result of relying on his inventions.
When Victor challenges Wallace to hand-to-hand combat he insists that they follow "Queensberry Rules", a traditional set of rules for boxing, one of which is "no rabbit punches" (a blow to the back of the head).
Constable Mackintosh's insistence that the damage to the vegetables was arson ("One of you, arsin' around!") makes sense when you consider both Anti-Pesto and the competition's track records. The former's pest control devices are repeatedly proven reliable and effective in the movie, particularly with their anti-pest surveillance network letting them rapidly identify and respond to issues (as seen in the introduction.) For them to suddenly start failing to protect their owner's vegetables from regular rabbits just before the festival would be a very suspicious coincidence in itself; coupled with the constable's claim the competition has led to trouble between the villagers each year due to them treating it excessively seriously and the signs that something much bigger than your average rabbit caused the damage, a disgruntled or unethical competitor sabotaging their opponents becomes a very real and logical possibility.
When Victor is getting the gold bullets from the vicar, the older man delivers a speech about the bestial side in everyone, much to his audience's annoyance. As Victor leaves, the vicar cries "Beware! Beware the beast within!" Considering the horrific lengths that Victor employs to get rid of Wallace, he didn't heed the vicar's warning.
When Victor left Tottington Hall near the beginning, he had a rabbit on his head that he mistook for his wig. However, when we see him next at the church meeting, he has an identical wig and the rabbit is nowhere to be seen. Considering that he originally wanted to shoot the rabbits dead, it's not too far-fetched to guess that he killed the rabbit on his head...unless the poor thing was wise enough to escape before he noticed.
Assuming it isn't just a case of Wallace gaining awareness once he realizes what's happened, scenes where he seems to have some of his old mind (e.g., at the end when he got angry at Victor Quartermaine hurting Lady Tottington and how he recognizes Gromit), there is a chance that it's a Superpowered Evil Side for Wallace at best where he loses himself to his rabbit's instinct or at worst an And I Must Scream situation where he could see and know everything that happens around him yet can't do anything until he fought back against it.
puts into perspective why Wallace was gaining weight in the first place. Not because he was getting older and not just because he was eating lots of cheese, but mostly because his automated lifestyle meant Wallace wasn't exercising enough. He doesn't even use the stairs to come down. If anything, his weight gain is a natural result of relying on his inventions.