I have good news and I have bad news.
The good news is that it is possible to run multiplayer games using mods such as added nation mods. The bad news is that it is not possible (as far as Ive been able to do) to do it by automated script or text mode. There is an --enablemod switch which will turn a mod on but the mod doesnt get checked in that mode until the game-creation stage.
From the tests that I have done I think you can probably use enablemod with the banners mod, the heroes mod, the balance mod, and various mods that turn off spells or equipment that people dont like. It seems to only be nations that are a problem.
The work around is an extensive setup by the game host. A combination of PbEM (the players send you their gods), hotseat game creation (you make the game and "join" as each player), and then shifting it to TCP/IP. Its the best we have come up with so far and seems to be working in the mega-game Perpetuality altho I wouldnt want to do that very often.
Check out this thread...
Single Age mod
edit: I should mention that it has been reported to Johan over in the beta-test group.