NodePath.setCollideMask() adjusts the into collide mask of nodes at that node level and below. It is the method you should call most of the time for ordinary nodes in the world.
PandaNode.set[Into/From]CollideMask() adjusts the into or from collide mask of that particular node only. It does not traverse below to children nodes. It is the only way to set a from collide mask on a node that you are adding to the collision traverser; but there’s not usually any other time to use either of these methods.
David