The process is basically no different than that via Finder. You can continue to use iTunes to backup, update or restore your iPhone. On a Mac with macOS Mojave 10.14 or earlier, things aren't changing. mobileconfig file extension that defines device settings, such as wireless network and VPN configurations.
Instead of just dumping your Documents and Desktop files into your local Documents and Desktop folders, where they could create quite a mess if you already have files there, it puts these in these iCloud Drive Archive folders so you can look in them and figure out what to do with these files orphaned by turning off iCloud.
The iCloud Drive Archive folder appears when you turn off iCloud Drive.
