When we lived in NJ, I was towing our pop-up North on the Garden State Parkway. There were signs that EZ Pass users that are towing should stop at an attended toll booth, so I did. The toll taker looked at me weird and said "you have EZ Pass" and waved me through. After that I never stopped. I've towed through NJ, PA, DE and MD with a Pop-up and a Hybrid TT never stopping at a toll again. Never had a problem with being charged wrong, but I'm sure it happens.
None of these states had Hi-Speed EZ Pass at the time, so I don't know if that works differently.