Hi all,
just registered to maybe provide some information on this. I know very little of the Kindle Touch software stack, I've just been doing some reading recently, I don't own the device (yet).
Kindle Touch seems to be running the
Awesome Window Manager, so that is most probably the cause of the overlaying of the X apps by the Kindle UI. Awesome is configurable using the Lua language and there will be a rc.lua somewhere on the filesystem that defines the rules for displaying the applications.
Here is
rc.lua posted by a user to the Awesome mailing list (
the thread). From the looks of it, they are using a modified version of Awesome with the rc.lua also containing a lot of custom code and quite some number of hacks. Your issue is most probably hidden in there somewhere and could be changed.
That is also the place that handles all the input before passing it to the applications, so any global shortcuts can be placed there - like taking a screenshot, you can find the code for that in there. All in all, you can do a lot in that file, making it a great and easy way to mod the device.