Humm, New York E-ZPass can be transplanted into any vehicle of the same class. I had one that I was using for a few weeks before I "registered" my licence plate with them, as I was waiting for them to mail me my PIN numbers to access my account. The CSR on the phone said that as long as the E-ZPass is valid, they don't care what car it is in.
The same goes for Ontario's Hwy 407ETR. The only caviat is that if the transponder isn't read it will generate a bill to the rental company, who will in turn hit you for it plus a surcharge to handle their time and effort to figure out who had the car that day.
As for why not have an E-ZPass for the rental fleet, cost is probably a big issue. The amount of pre-paid tolls has to be pretty hefty.