The port to which to connect can be overridden using a FreeTDS extended syntax.
A port may be appended to the servername in the form  servername:portport must be a number; a service name is not supported.
If you specify servername\instance
Note that other freetds.conf properties still apply.
For the technically curious: each Microsoft SQL Server instance appears on the network as a server listening at a port.
The old way — and it still works — is to designate each instance in freetds.conf as a separate server.
The new “named instance” notation, if we can call it that, instead uses the server to discover the port.
The library sends a UDP packet containing the instance name to the server at a well known port, port 1434.
The server responds with a port number.
FreeTDS then uses that number to connect in the usual way.