(passive) notification popups that time out are quite useful, but only as long as the user is actually paying attention to the device. therefore, i think it would make sense to postpone starting the timer while the user is apparently AFK. i suppose the right way to detect AFK would be KIdleTime reporting >15 secs inactivity, no simulated user activity, and no screensaver inhibitors being registered (i'll note that the fdo screensaver d-bus spec currently offers no way to query that).
I think this is a good idea. Would you be interested in submitting a merge request to implement it?