This is quite a common issue. Not just with one drive but any file sync software that syncs your users directory.

It doesn't matter where you install the game all the user data will be still bebstored in your mygames folder.

If you want to use one drive just create a couple of exceptions (ignore list) and tell it to ignore both the logs folder and ffxivpatch folders.

It's a pretty common reason why people's updates can be slow because one drive or whatever is trying to sync the ffxivpatch folder while the game client is making changes to it and causes conflicts.

Disabling it entirely might not be a great idea if it's your only real backup.