I just checked now, and it's as I suspected. The game first checks for %LOCALAPPDATA%\Indiana\Saved\Config\WindowsNoEditor\, and if it doesn't exist it created the %LOCALAPPDATA%\Packages\PrivateDivision.TheOuterWorldsWindows10_hv3d7yfbgr2rp\LocalCache\Local\Indiana\Saved\Config\WindowsNoEditor\ folder.
Probably no one else have both versions, so it's indeed either the one or the other for most people. I'll update the path!