The bill by plate would only come into play if there was a failure to read the EZPass transponder. Entering the plate number in your EZPass account is only a fallback. Worst case when you didn’t enter it and a transponder read fails, you get a chargeback from the rental car for the toll(s) plus whatever convenience charge applies for the particular rental car company you used. These can vary to a charge just for any days where tolls were charged to a daily fee for every day of the rental even if you did not incur any charges on some of the days.
I don’t know what the transponder read failure rates might be for EZPass transponders. I’ve been using the Illinois version of EZPass (known as IPass) for many years (more than 20, with a transponder upgrade a couple of times in that interval), and we have a lot of toll roads in the Chicago area. I routinely monitor charges to my account for the two transponders we have in our personal cars. I have never noted a transponder read failure. I’m actually surprised at the apparent reliability over time. I don’t know if the Florida readers are as reliable, but it’s nice to hear a report of no problems where the plate was not registered in your account. I wonder if it would make a difference in the Miami area where toll by plate appears to be the norm, with no cash lanes that I have seen when visiting.