LR was designed to show the metadata status based on the actual contents of the metadata fields stored in the catalog and in the photo's file, ignoring the file's date-modified. When LR notices a file might have changed on disk (using the file's date-modified), it compares the catalog metadata fields with the file's fields, yielding these possible statuses:
Up To Date: The catalog's fields match those in the file.
Has Been Changed: The catalog's fields have been changed but the file's fields have not.
Changed On Disk: The catalog's fields haven't been changed but the file's fields have been.
Conflict Detected: Both the catalog's fields and the file's fields have been changed.
So if some other program changes the file's date-modified without changing the metadata fields, normally the status doesn't change.
You can see how this normally works by using Exiftool to change a file's EXIF:UserComment field. If you use Exiftool to set that field to its current catalog contents (thus changing the file's date-modified but not the field itself), LR continues to show Up To Date. Only if Exiftool sets the field to a different value does the status change. (Be careful if you test this yourself -- once LR changes the status from Up To Date, it never goes back to Up To Date until you save the metadata or read it from disk.)
But LR's metadata status has always been buggy (at least since I started with LR 3). The most common complaint over the years has been about spurious Conflict Detected -- the user has definitely not made any changes to the metadata fields, but LR thinks differently. I get some of these every year, it seems. I do Metadata > Save Metadata To File to get rid of them.
It's been very difficult to spoon-feed Adobe with a tidy, simple recipe for reproducing these bugs, and Adobe hasn't paid much attention to them. But
one particular bug introduced in LR 10.1 is easy to reproduce: LR doesn't properly handle reading crop angle from the file's metadata, and it shows incorrect status.
(Old Car Talk fans might remember Click & Clack's recommendation to cover spurious engine warning lights with black electrical tape so that it wouldn't annoy you :->)