It seems like a harder problem than that as well - you might want some of the units in the back of the swarm to go the long way because they'd wait a long time

It seems like a harder problem than that as well - you might want some of the units in the back of the swarm to go the long way because they'd wait a long time at the choke. But maybe you don't want to do that - those units in the back are squishy and need to stick with the units at the front of the choke. But maybe that's ok - the alternative path isn't too far away and it's not a risky move to make. Maybe that's too complicated. Probably best to make the swarm operate as if other moving units don't exist (to make pathing predictable) and let the player micromanage via waypoints/grouping.