Is it possible for my app to "take over" when a system alert pops up? My app disables the idle timer, but when a system alert pops up, the alert seems be enabling the timer. What can I do about that?
Are you trying to suppress the alerts? Then the answer is: you can't.
If you're trying to prevent the alerts from messing with your app's disabling of the idle timer, then I believe donkim is on the right trail.