> in the end the Find My beacons have to resolve down to some common identifier otherwise the "an unknown device has been following you for 2 hours" warning would not work.

Not really, this is actually pretty easy. If such a device beacons and a trusted device is within range the trusted device can respond to the beacon and let it know it's nearby, then it just counts up if not. X number of beacons with no response, set the "not near my trusted device" flag. Some other device sees X number of beacons with that flag set while moving around, send alert to the user.