(apologies for a non-answer reply)
Haven’t experimented with SFTP between machines, but the flyctl code may have pointers for you.
Why not consider deploying LiteFS instead? Or, wait for a managed LiteFS offering, which should be right around the corner.
There’s turso.tech and Cloudflare D1 if you want a managed sqlite3 based database right away.
Fly 6pn works out of the box. There’s nothing to configure, as such. Listen for incoming requests on fly-local-6pn and the server should be able see requests over the private network setup by Fly. Ref: Can't get a CouchDB Cluster working (connection_closed) - #4 by ignoramous