I think there is a misunderstanding here. I believe that michaeljt is indicating that _only touch pad_ gestures would automatically go to the currently focused window. While it's clear to me that with a touch screen one can interface with any window the user touches.
Thus we are convinced that touch screens and touch pads will have diverging code paths and it would be possible to implement a fix or feature in one with out effecting the other at all.
Thus the solution is to have private zones for a touch screen and use the existing key board locking for a touch pad.