Let me expand on why modifying the original files is (IMHO) a bad idea, independently of my proposed solution.
When you edit an image, you should keep the original version anyway, because otherwise you are going to lose information. In this case, you are not modifying the original file, but creating a derived work (for which, I agree, you would want the same tags applied automatically based on some image matching algo).
If you change multiple copies of an image independently, you need to merge those changes somehow. Basically, you end up with the problems concurrent revision systems solve (and the complexity that entails). Merging two database tables with a common simple structure is a trivial task.
Deduplication is much easier if files don't change. I have the exact same file in two directories: delete one copy. I have two files with an almost identical image but different tags, cropping or other. That needs manual intervention and is error prone.
Twenty years from now, I prefer to still have the picture I took, rather than a version with some cropping, some sepia filter applied when I thought it was cool, a few rotations randomly applied by the image management program du jour and a re-encoding or two for measure. I'd also rather avoid relying on the backup software I used twenty years ago and I may have stopped using in the meanwhile to retrieve a previous version.
Having said this, it's as usual a question of compromises. Just use the one which better works for you and your workflow.