It only needs to be registered if for some reason it can't read the transponder and needs to figure another way to get payment (by the license plate). If the car isn't registered, you have a hefty fee attached to the toll, if it is, they assume it just didn't read, and it's just the toll the first few times it happens.

I went two years on a new car forgetting to register it, and only had a problem when it coulkdn't read it and sent a ticket. Then I realized I never registered it.

A phone call fixed it all, but as long as they can read the transponder, they never need to know anything else about the car.