good question.....we has been experience before.it will be depend to the installer how there do it. but the correct way is arm the alarm then the engine still running after just switch off by the timer.
It's not about Airtrek but more in general. My Airtrek comes with clear windows (local USF car), but I've tinted the rear doors, rear side panel and rear windscreen 75% tint. Using it for 4 years now, no problems...