Earlier quoted context omitted.
Adding an interface to access the tag store won't be very hard. It would be harder to make it so that all the tag-oblivious programs, like mv or vi, to say nothing of rsync, would preserve the attributes when moving or modifying a file.
Sidecar files might work, and would also be filesystem-portable.
I have to deal already with these on file shares, specifically for Apple: .DS_Store, .Trashes and .AppleDouble, or for Windows: Thumbs.db, $RECYCLE.BIN (for some reason Windows sometimes ignores the fact I've disabled the recycle bin on a share and creates this instead) and desktop.ini. Please don't drop crap around directories where there exist a multitude of tidier alternatives.