That's completely logical because the payments part of AP knows nothing about the loyalty cards part.
Deleting the app makes it much less convenient to look up and load offers. It also makes it much harder to do a points inquiry.I ended up adding the barcode from the Android app to Android Pay, then deleted the app. I now just show the card to scan within Android Pay then switch over to my PCF card to pay.
I think I'll stick with double-tapping my PC MC card. That's convenient enough for me, at least compared to the alternatives.