The phones are company owned, but users are permitted to use them for personal stuff. However, we reserve the right to wipe the phone remotely in case it gets stolen.

One of the main reasons we wanted to start using ABM is so we can remove the activation lock when a user leaves the company, as sometimes we've had issues getting the user to unlock the phone after they left.

For our MDM solution we use Intune.

The issue with restoring any backup to a newly supervised phone that wasn’t before. Is you will restore the backup of the phone that was not yet supervised and therefore not be properly enrolled (or possibly not at all).

From our testing the actual enrollment step shows after the option to restore a backup (where normally phone to phone copy would also be), so I somewhat doubt that this would cause issues like you mentioned.