Could one of the model guru's perhaps take that beat up old Highwayman and throw an engine and some tires on it? Is there even a 'functional' car model in the game that could maybe be substituted?
This could be a trigger to permanently (if not already done by the mod in the first place!) shut off fast travel, and only allow it by activating the car.
The trunk would open to a linked storage chest that doesn't respawn.
The hood would be an activator to check fuel levels and insert MFC's as needed.
A quest for the car could be triggered by clicking it's static model after finding it, and would involve finding 4 tires, a steering wheel, some electronics and of course...fuzzy dice.
Of course it goes without saying that someone should also port over one of the 'fatboy' motorcycles from FO3 that was used in the same fashion and enable it as well...maybe find a motorcycle and fix it early in the game, and the highwayman much later as chance (and memory) permit.