I did a check on the modified time of the file. The upper image is a manual save and the time difference is 15 seconds.
The lower image is an automatic save and the time difference is 3 seconds.
What is the time difference limit for LR to when to set the photo as externally changed for the date modified?
I have the exact same problem after I merged a number of catalogs to a new one. The files reside on a fixed internal disk in a Win10 64 bit system.
Did you find a solution yet to this mystery? Does it matter at all? I have no idea.
People have reported spurious "metadata changed" and "metadata conflict" notifications since at least LR 3. If you're sure that you're not changing the files' metadata with an external program, it is safe to ignore the notifications.
There may be multiple causes of this problem, and Adobe has for sure fixed at least one or two of the causes years ago. But given how long the bug(s) has been outstanding, it's unlikely to ever get fixed in my opinion. See these bug reports: