Other than the buses shared among the Epcot resorts, the only regular, direct resort to resort bus that existed with Boardwalk was a bus that ran between Boardwalk and Coronado Springs during the late afternoon through evening, which was discontinued several years ago. Why there was a bus with Coronado and not any other non-Epcot resorts was never fully explained except for mention that both had convention facilities. I do not actually know whether the Coronado bus was included in BWV's transportation dues but I suspect it was. However, when the bus was taken out of the system, transportation dues did not decrease and still rose somewhat annually. They have in the past sometimes had the late night (e.g., post midnight) Downtown Disney bus from Boardwalk stop at some of the resorts other than the Epcot resorts but I do not know if that still happens with the Disney Springs bus.
What I have never been clear on is the limitations of the transportation item in the dues. It definitely applies to any transportation systems dedicated to the particular resort, but does it also include some fraction of the sytem as a whole? For example, does a portion of the Boardwalk dues apply to the monorail on the theory that some of those staying at BW are likely to make some use of the monorai.