Whether the fasttrack or FastPass is paid for or inclusive I still think Disney have it right with merge points. Basically,
don't let anyone enter from the exit side,
make at least the standby or FastPass line wide and not snakey so wheelchairs can use it (therefore only people with autism etc need to use the return time system, wheelchairs can wait in the standby or use FastPass),
make the two queues merge close but not quite at the station,
where possible add single rider but make it arrive on the same side of queue as the airgates so you can batch the singles in with everyone else before the car/train arrives.
Oblivion is one of the better rides for single rider merge as they have the space for batching two trains worth so can plan ahead. Nemesis couldn't add singles until almost ready to despatch so it slowed throughput slightly.
As others have also said, adding fasttrack from the exit side of station will result in needing to close rows off (same as Vampire at CWoA), which isn't an efficient way of batching really.