Normal PE authentication just relies on LDAP talking to AD/Directory for user/group enumeration/auth whereas Files performs an actual machine account 'join' operation for the files instance.
There's more clever involved where Files AD join is involved updating SPNs/DNS etc so individual FSVMs can be the files instance name etc for clients and similarly in a SmartDR scenario where the Identity of the files instance is brought up on the DR side for clients to get to their data.