I found a description of the command line options to run the game in skirmish mode. I also figured out how to set up the game options and forward my settings.
Can I somehow open the game in lobby mode, adjust its options, but not launch it immediately?
The /hostgame command doesn't seem to work for this case.
How open Supreme Commander FA Lobby (Skirmish) via command line?
I think something like this is probably what you're looking for:
C:\ProgramData\FAForever\bin\ForgedAlliance.exe /init init_faf.lua /nobugreport
This will launch the game with the FAF modifications enabled, at which point you can open a skirmish lobby.