A person at the counter was vaguely scaring me that my own NY device will not "work out" going immediately under I-90 readers.
I use a NYS Thruway EZPass on a regular basis with rental cars in MA and have a success rate of about 99%. If there was some recent policy change it was not in effect last Sunday, as I just logged in and can already see a MassPike toll from January 7th on my account. I did have a bill for a single I-90 segment sent to the rental company's contractor last summer and they tried to bill me $1.25 plus a $24 service charge, but they (think it was ATS/Platepass, so probably a Hertz rental) quickly refunded it when I e-mailed them a screenshot of my NYS EZPass account showing that I had been using my own transponder that day.