To be fair I don't think they ever claimed to be 100% accurate, because it requires participation from entities beyond their control. Perhaps the service writer or the owners of the dealership where you had your truck maintained had the same attitude about carfax as you do?
That one with the three doors of other colors sounds like "under the table" dealings to me. They fixed it with junkyard doors and didn't report it to the insurance company.
I've never purchased a carfax report with the idea that it was all-encompassing, and have no idea why anyone would. It's just a tool, and better than being totally in the dark. Pretty sure they offer a money-back guarantee if they're wrong. You just have to ask for it.