I would like to have a "Disable Check In of _V folders" setting:

If you have your Windows File Explorer set to show "Hidden items", and you add folders and subfolders to Vault with drag-n-drop, then _V folders will be added to Vault. And writeprotected on disk. This messes up with the functionallity. Things behaves strange, and unexperienced users can't figure out what is wrong.
I think the default setting should be "Thicked".
During check in you should then have the opportunity to "Skip these folders and continue with the rest of the files".