You can easily do shader that contain multiple effects and then you just choose which one use per pixel.
Believe me, in this particular case I can't. The insight reasons for this would be off-topic here. Just think of instruction limits.
I don't think that's what he wants. He seems to want all or nothing based on screen contents. Still not sure I follow on the contents though. From my understanding, the boxes aren't actually "there", as in they have no drawn geometry. You can stand inside of them, in which case the filter/effect should not be applied?
Right. The "box" is not being rendered, it's only virtual, a defined area in which something happens. No "physical" object to be drawn. The box's sole purpose is to serve as reference coordinate boundaries in which a certain effect will take place.
Maybe I'm being stupid here, but how can you define a non-aligned box by just two points?
Well, it's an approximation. Think of it being aligned if it helps.