My use case is I’m transferring large already encrypted files between two servers connected via wireguard.
Is there any benefit to SFTP over FTP in this case?
Personally, I always use rsync for these sorts of jobs. Works over SSH so don’t need anything on the server except SSH, if the trasfer gets interrupted it will resume from where it left of. Overhead from SSH is pretty minimal, but if you really want thigns to go as fast as possible, you can setup an rsync server …
If you don’t want to use rsync, just use SFTP or SCP.
FTP will go a bit faster since you won’t be adding yet another layer of encryption, or the performance issues of openssh. If you’re certain no one will be sniffing your FTP creds before or after they pass through the Wireguard tunnel, then I’d choose speed for large transfers.