If you have it enabled such that you can see your vehicle info in the app, them yes Ford can see anything the vehicle records, IF they know your VIN. The app software doesn't let you do all that, but Ford can because you consented by enabling the data transmission. So, for the "convenience" of the app functions, you allow Ford full access to all your vehicle data. They can't see a specific "tune", but they can see the reflash date/time and the key cycles, to deduce there was something done to the vehicle. There's one thing I don't know about and that is if they can see the current calibration number of the data loaded. It's likely possible, but I can't say.
Note that you can turn that vehicle access OFF in the vehicle SYNC menu, but you lose the capability as well.