We have used EZ Pass in NY and elsewhere since it was introduced. No matter where we go, with or without the trailer, we use the same transponder. Never had issues of wrong charges and were told by the powers that be that sensors determine how many axles and not the transponder. We do have separate transponders for each car but not for towing and not towing. Even going through the new toll road in NC one day with the trailer and two days later without it got it right.
I would suspect they like making tiny amounts of money on the money that is held by the system for each pass.