High capacity doesn't mean lower flow on its own--high capacity that's being *fully utilized* can mean lower flow though, at least for roads. But parking garages for long-term use? It's not like street parking where most people will stay for 5 minutes...
Similarly with seats on trains--the flow has more to do with number of doors, level platforms, and width of center aisle on board. You want high flow/capacity on trains, you want longitudinal seats with lots of standing room, NOT unreliable prices for seats