> Transferring files shouldn't involve that central server, so you'd need to establish a direct connection between the users

That's exactly what Galene does when a user requests a file transfer.

> with network topologies those days, it will most likely require a relay between the two

We perform NAT traversal by using the server to punch holes in both NATs. Only if that fails (due to a symmetric NAT or to an overly restrictive firewall) do we fall back to relaying through the server.