I would not worry about it, on my car the immobilizer is only deactivated during the starting sequence, and reactivates after that car is started.
I installed the starter myself and before I programmed the keys I played with the system a bit. I sat in the car and started via remote, the car started fine, I then put my unprogrammed key in the ignition, turn it to ACC position and tried to drive off. The second I pressed the braked pedal my car shut off and sounded the alarm.
But you have to be careful, as some remote starters require a programmed key to be hidden in the dash to deactivate the system, these types of starters will deactivate the immobilizer permanently, so look for ones that have a programmed module for this purpose.