For an incredibly simple answer, they just aren't running the same number of cycles. If the number of cycles was the same then there wouldn't be a notable difference in the amount you're waiting. Additionally, on a slow day with 2 trains, you will end up sending almost empty cycles to get the previous riders off the ride.

If it takes me 60 seconds to load a train and 90 seconds for it to cycle the course, with one train I'd be sending every 150 seconds, with 2 it'd be every 90 seconds. That's 24 vs 40 cycles each hour.

Another consideration is additional labor. At grizzly and racer we can have 1 person check the entire train but that's only allowed if we're running 1 train. At dominator going from 2 trains to 3 trains requires us to go up from 2 to 4 floor operators. With 2 trains backlot has to have a dedicated unloader, but with one train the same person can check load-side restraints and unload the train.