All it is doing is modifying the collision of each building to tell them to collide with the hovercraft. The mod can't use existing collision layers because the hovercraft has unique collision in that it needs to collide with buildings but not with water.
That said, I've just taken another look at the collision masks in 2.0 and I think it might now be possible to get the correct collision on the hovercraft without creating a new collision layer, just using is_object, train, and car collision layers. I'll have to investigate tonight - collision masks are a delicate thing.
