I did it to remove a tiny scratch on my (sports) watch - the only time I even notice is if the watch gets wet, water doesn't "repel" from the area with no coating like it does from the rest of the screen.
In theory, that little area will technically show fingerprints more - in reality, the damn thing is always covered in fingerprints anyway.
It's not a "fix all" solution, and won't work in all situations, but if the scratch is only in the coating it should get rid of it. It shouldn't affect the scratchability of the screen as the glass is unchanged.
Perhaps it's just me, but the Saphirre display doesn't seem to collect fingerprints as much as the Ion-X Glass does on The Sport Watch.