I thought the "Administrative Fee" was to punish people who do not use the rental car agency's toll billing service and just go drive through the toll booths mindlessly...

It is a bit unfair with cashless tolling but I have had a few situations where I have paid the toll by going to the tolling authority's website and entering in the license plate, etc. to avoid the rental car company getting a toll violation notice and avoid this sort of surprise "Administrative Fee."

Best strategy is to plan ahead for the toll roads. Either decide if you will use them or not and plan accordingly. It is a hassle but as government and government-like (private "toll road authorities") units keep building themselves up more and more it seems that the toll road thing is going to only get more and more common/popular.