Yep, that’s the problem and in those situations it won’t work. (Maybe CG could implement a priority attribute, so we could just choose? Dunno if this could work.)
It’s a good thing, when it comes to setting up renderlayers. There you can just override the “Disabled” flag on one set and enable another one. It’s pretty handy when you need to rerender parts of your scene.
But yes, more then one VOP per object on a single layer is crap right now.