If you're going purely for capacity, I would assume the transfer variant is faster. Separate unload/load will take longer because riders cannot simultaeously enter and exit the same train. First the entire unload station has to be clear before the train can advance. Meanwhile the station with the transfer track can open the gates while guests are leaving the station platform. In addtion to that, there is also the time it takes the train to go from the unload section to the load section.
Now, I think the difference is not all that big, plus I've had to make some assumptions. For example, if the transfer section takes a lot of time to switch, this could greatly reduce the capacity of the ride. Or the park could have a policy where the gates should not open before all the other guests have left the platform.
Now, if you look past capacity, the separate unload/load stations are less hectic than other variants. In stations where unloading and loading takes place at the same time, it becomes kinda chaotic and difficult for the operators to keep an eye on everything, (I've seen operators open gates at the same moment the restraints are released, complete madness). It gets especially bad when there is only a small area of a very long station where bags may be placed.
Talking about bags. If you have a separate unload/load situation, you need to find a way to re-unite guests with their left belongings. Some german parks have a double-sided closet/cabinet. One end connects to the station, the other to the exit path. Disney requires you to take everything with you and other parks simply ban loose articles past the queue entrance.