Disney encourages online check-in, which doesn’t ask if you will be parking a car. I agree they have some goofy enforcement policies but letting people drive into the resort in a car, check in in person and deny they have a car would be unfair and would definitely discourage checking in online.
I assumed they note it when you drive up to the security shack and produce ID. Is it possible you displayed the handicap pass on your rental when you drove in? Or that the CM noted it when you told them about the pass? It seems more likely that you weren’t charged for that reason.
Again, Disney is wildly inconsistent and I’m not doubting anything you say. But it would be an odd way to enforce parking fees.