While it may be cheaper to "get away" from the big name truck stops, but how much cheaper? I don't agree that truck stops charge upwards of 50-60 cents more per gallon on the main drags, but it's the connivence of things I guess. Sometimes the "RV" lanes at say Flying J can be all jammed up and no place to move where as trucks lanes offer multi lanes and room. At some stops, it may require to pre pay to release the pump. Like OP said, a PITA, but doable or have spouse/another person go in and do this while staying at the pump. Once fueled, pull ahead to make room for next person. If you want to take a break, pull out of pump lane and into a empty spot in lot. Some places have RV spaces, which are usually near the RV pump lanes or thereabouts. Wear some type of glove handling the fuel handles as some tend to be oily due to fuel.
One BIG advantage of getting fuel at a truck stop is that the fuel is turned over often and less chance of water in it if bought away from truck stops. Saying that tho, UNLESS you know otherwise or talk to others of where to get fuel away from truck stops that turn over fuel often or no known issues, stick w/ the truck stops.
It may be intimidating pulling into truck lanes w/semis all around you, and the semi drivers sometimes give you strange looks (not all), just don't dilly-dally after getting fuel and pulling ahead to pay, P break etc. Other than that, have fun and enjoy.