It's fairly easy to simulate collision between an upright capsule shape and convex objects. You just separate the upwards and downwards-pointing faces with a vertical wall, equal to the height of the shaft of the capsule, and run sphere collision on it:

However, this means you have one "heightened" copy of the map, which collides with players, and one regular copy, which collides with crates and things. Is it possible to mix the two, and still have the player affect crates, and vice-versa?
To clarify: Crates collide with one copy of the map, and with players. Players collide with crates, and a modified copy of the map. Crates to not collide with the modified copy of the map, and players do not collide with the unmodified copy of the map.

However, this means you have one "heightened" copy of the map, which collides with players, and one regular copy, which collides with crates and things. Is it possible to mix the two, and still have the player affect crates, and vice-versa?
To clarify: Crates collide with one copy of the map, and with players. Players collide with crates, and a modified copy of the map. Crates to not collide with the modified copy of the map, and players do not collide with the unmodified copy of the map.