Thanks Ashley - but I was hoping to avoid that (and I did, sort of). I managed to work around it by making the layout bigger and putting the instructions somewhere far off the normal viewport, and then I just scroll to the instructions, and then I scroll back to the game. This has the advantage that if I add something to the main screen, I don't have to remember to add custom stuff to it (hide it, check for visibility etc).
So it's almost what you suggest, moving the objects away, except I didn't move the objects - I moved the thing that was supposed to be on top of them, so they don't overlap.
However I still think that a mechanism to prevent the click or tap from "bubbling further up" (or in other words marking it as Handled) would be nice.