After much discussion with E-ZPassNY, they are apparently going to link a new "plate-mounted transponder" to my existing account so that the discount will be applied... they are well-aware that the window-mounted E-ZPass units won't work with Model S windshields... no "green" plate-mounted transponder, just a software link. They requested that I send a copy of my registration (which I did via Email), and they will be sending me a new plate-mounted transponder with a bag/return envelope for the present unit.
Aggravating part of experience was explaining to 4 service reps that, yes, my Model S was NOT a hybrid, but since it was an EV it was listed on the page as one of the vehicles approved for participation in the program.
Now, about reviewing my travels for refunds dating to the registration of my car...