Well, Apple is moving in the direction of syncing everything with iCloud - iCloud Drive has been around for a while, and Sierra adds the ability to sync the desktop and Documents folder; of course on top of long-existing things like photo sync. If the file was previously uploaded to iCloud, there is redundancy, and you definitely don't want to overwrite it with the corrupted version.
How big an issue this is in practice I don't know.
How big an issue this is in practice I don't know.