E-ZPass now has interoperability with the Central United States Interoperability Hub (which reaches as far west as Colorado and as far south as Texas). We're much closer to the point where you can drive anywhere with a single transponder than we were back then. The main thing missing now is California cooperating with anyone else.
I like the idea of my toll road account also being useful for public transit, if nothing else. But it's difficult to imagine toll road operators and public transit operators seeing a big incentive to cooperate in that way. Even though they're both "pay for transit," their intended/typical users are very different (people who can't/won't drive vs. people who not only drive but are privileged enough to pay for less traffic).
So really, you only need one state to adopt your unified transit fee idea.
Halifax, NS used to have bridges where the toll transponders worked to pay for parking at the airport - super convenient. Alas, they've since removed the tolls on the bridges, so the transponders are now useless and traffic in the downtown is even worse.