Interesting conversation.
I agree with blymi, this is a situation I have to deal with all the time.
Maybe a behavior could be created for layers, like "Intercept input", meaning actions could not pass through this layer and affect everything underneath (except what could be visible through transparent parts of the layer).
And "Disable input and obstacles when layer is invisible", meaning input could not be registered on this layer when it is invisible as well as obstacles won't be taken in account by pathfinding and physics.
What do you think ? Ashley, could it be implemented in a future beta ?