I find it to be a bit sketchy in general, because it means the OS is actually parsing and editing the actual bytes of the file contextually when an app tries to access it. Probably making a shadow copy somewhere without the GPS exif data.
But yeah, I agree, at a minimum the OS should pop up a notification that “By default, GPS data will be stripped from the file due to inadequate location permissions” until the user either changes their preference or says “that’s fine, don’t remind me for this app”. Having it happen silently just isn’t good.