Ed,
I realize AP is easy to switch with, but you really don't need to go back and forth to 'stock' every time you go to the dealer. Before I bought my '05 STI, I spent a while speaking with a Service Tech, Service Advisor and even the Service Manager @ Goldstein...I wanted to find out just what the SOP was upon a visit to the Service Department. According to each person I spoke with, there would be no reason to do diagnostic scanning that would indicate your car had been modified with AP, unless you had a CEL of some kind.
On another note, my only regret is that I had AP stage2 installed on my STI 2 days after I bought it, so I never knew what a stock one drove like.