Any time a car owner makes modifications to a car, that changes it from the original specifications, they better be ready to do their own service on that modification. Or they better be prepared to very clearly communicate, to any shop that they take their car to, what modification has been made, and what the new specifications are.
It is unrealistic to expect anyone else that works on a modified car, to recognize the modification, understand what changes it makes, and know how to address it. Particularly at a place like a quick lube shop.
I agree that a good auto mechanic should have read the label on the cap. But lube bays aren't staffed by good auto mechanics. They are often staffed by kids that think they are real mechanics, but really only know the basics. And the work order says to put filter A on, so that is what they do.
If the Jeep owner knew that the filter housing takes a different filter, and did not tell the quick lube shop, then he needs to understand that this is his mistake, and accept the consequences.