Nailed it! Sharing my solution:
Download the file for setting up a server:
https://github.com/xerxes-at/T6ServerConfigs/archive/master.zip
Extract the files in a sub-folder of your Plutonium installation. Let's say is ./t6_pluto.
Create a server in https://platform.plutonium.pw/serverkeys
Edit ./t6_pluto/!start_zm_server.bat and add the key. Also set the correct path in 'set gamepath.'
Run ./t6_pluto/!start_zm_server.bat and then plutonium.exe. Select LAN Mode. Press F10 to get rid of the servers window and then hit the tilde key (~).
Execute '/connect localhost:<port>', where <port> is the one indicated in the console window (just switch with ALT+TAB).
Leave the game. You should now be in the lobby and able to join games. But just to be sure, exit the game, re-enter in LAN Mode, and choose 'Online'. If you're able to select 'Custom Games' you should join sessions successfully with '/connect masterIP:4976'.