This is what I've learned through lots of research on this site and the iwsti forum about Stage I AP and what Subaru can and can't see. This includes first hand accounts from a few of the more "honest" Subaru techs on the forums:
1) Subaru can tell if the AP is installed.
2) Subaru can not tell if the AP has been removed. The only indication on the ECU code is the "check sum value" (CSV). This is basically a log of motor starts. When the AP is removed and the orginal tune reinstalled, the old CSV value is posted to the ECU. Depending on when you installed the AP (right off the lot or years later), the CSV value could be a small or large. The CSV value is reset EVERY time you disconnect the battery. Many will say Subaru will question why the CSV value is low (compared to mileage) if you bring the car in with a motor problem. This is easily refutted by the car owner by simply saying the battery was disconnected recently to do a multitude of maintenance related tasks which specifially state unplugging the battery is necessary for safety. The owner must be quick thinking though when stating such information when questioned.
3) Open source tunes can be seen when installed and AFTER removal. The open source tunes do not have the ability like the AP to take a "snap shot" of all values of the prior tune and replace to stock. Certain lines of code don't match and that's Subaru's evidence of tampering.
4) Bring in your car in with an aftermarket downpipe and your chances of warranty go down expotentially.