Mpnret noticed your from Chester NJ, I hail from Long Valley! Used to love Chester bakery till that place closed up.
Hate to high jack this thread but I wanted to clarify as I'm having a similar issue. Just had a RS installed by a well known shop on my '15. Works great only issue is when I start and unlock the car from the RS it sets off the factory alarm. If I was to start it and then unlock from the key it does not go off. I usually always lock the car from the key and not the RS. If I use the RS to lock it, will this avoid the car alarm being armed? There is a bypass installed and I did not give up a key.
Nice to hear from another local Outback. My RS is a simple one button (no door lock/unlock). From past experience the more complex the RS is (door lock/unlock, temp display, alarm interface etc) the more issues pop up with the install. Also I don't understand the need for a lock/unlock button on the remote being the key is always in my hand as I approach the car and there is no need to unlock it from 2000' away. It does sound like your RS remote door lock/unlock is not interfaced to the factory alarm and may not even be possible. Maybe someone else with your setup could comment on your questions. As far as you question goes about the alarm not being set with the RS start button, I bet this is the case. You can test this by locking the car with the RS remote and unlocking the door by inserting the key in the lock. If the alarm is set it will go off. Either hit the button on the factory remote or insert the key in the ignition to silence it. Repeat the process locking with the factory remote and I guarantee the alarm will go off.
Forget everything I just said if you have push button start.