This ^. Wherever I go that takes EZ-Pass, my personal transponder comes with and goes on the windshield with the rental company's closed inside their RF-shield box. EZ-Pass appears to preference transponder over license plate (the plate is a backup if it doesn't detect a transponder for any reason). On the handful of occasions a rental company has charged me a toll, it's been relatively easy to reverse the charge by providing my EZ-Pass statement showing the toll charge to my personal transponder.

PlatePass through rental car companies is light-years better than it was years ago; used to be quite a racket, with exhorbitant "administrative" and/or "processing" fees often totaling many times the actual toll. IIRC Hertz (and perhaps Avis/Budget) got spanked pretty hard with a class action some years back and were forced to end the practice; now they can only charge the actual toll and a modest daily fee if you 'activate' the transponder by using it during your rental period. That's still an annoyance, but far less egregious than it once was.

YMMV for toll systems other than EZ-Pass. I have little experience with them and don't know if/how transportable or affordable a transponder for them would be. Some use RFID windshield stickers, which wouldn't seem easily substituted.