That sounds like a brilliant thing to have working, that's about the only reason I keep my systray showing, so I can see when Trilly is flashing at me. But I expect if such a setting did exist, for general systray icon flashing detection it would go off every time my internet connection or network connection icons flashed their screens to show data being transferred and that would just be pointless...
But if it could be targeted to just the apps you select, such as Trilly and PrintMonitor it would be great!
Sadly I know nothing of whether it is or could be possible.