The AMA rulebook states:
Motorcycles and ATVs must use the crankcases of the production engine.
Which is a silly rule that someone should submit a request to get removed. Note that it's the same for motorcycles and ATVs.
On the other hand, as I've pointed out before, there are no ATV hillclimb classes listed in the AMA rulebook...just like there's no Micro Mini class listed either. Therefore, any such classes are by definition exhibition classes...and since exhibition classes are at the discretion of the promoter, I'm going to reckon that his cases aren't going to pose a problem.
Also, the AMA hillclimb rules have this entry:
Open multi-cylinder motorcycles that do not conform to Sportsman standards. In this class, multi-cylinder motorcycles of all engine sizes run without handicap.
...which, I believe, could also be applied to ATVs such that if an ATV is found to not conform to Sportsman standards (like, maybe it doesn't have stock cases), then it has to run in an "Open" class - which *might* a class defined as "ATV" without displacement limits is an "open" class. Or, if the class was called "2-Stroke ATV" - or if it was "Veteran ATV"...so long as it wasn't displacement capped, it might be considered an "open" class. If the class was called "ATV Open" then definitely.