
Amm yea, actually, Classic is of course not that compatible with everything as, like you mentioned, map1 has a default map_config.xml with all three factions included and Classic 0.88 script assumes all maps are 2-faction battles.
Anyway, in 0.89 in the actual game build, map_config.xml has minimal meaning on topic of factions, as the player uses the menu to create a new custom map config in the end. On servers, there's of course no such UI to create the config, so the two options are to create a map config on fly to be given to the server at change_map -command in the script or use the default map_config.xml like previously and adjust start_game commands in the script to reflect that (the reason you had crashes with map1 in Classic was that start_game only declared initial settings for 2 factions, while map_config.xml was set up for 3, I'd guess).
So, what does this actually mean?

Well, I've now set up Invasion script so that it uses custom map configs for each map, created in the script. Mostly it just makes map1 and map5 played in 3-faction mode, but later certain maps will be played between Green and Grey, Green and Brown, Green and Blue and Black, and so on, so there's a linear way how it's going to be based on the stage the invasion is in. This mostly doesn't concern server admins much, as they most likely want to run Invasion the vanilla way, if the want to run Invasion in the first place.
Classic however has much more variety in how it should/could be set up thanks to the custom map config, and frankly, I don't even know what to do with all this. The thing is, do you want to set up all maps for 3 factions or 2 factions, and if 3, do you then leave Al-Tabul out of the rotation as it has been designed for 2 factions only?
Also, if you enable persistent profiles for Classic, and sometimes don't include all factions in the maps and sometimes do, then the players who exit a map being Brown, might have a problem entering a map which doesn't have Browns. I at least know I didn't try what happens in such a case.

Bah, I guess I'm setting Classic for 2 factions only, it should be easy to hack it into other solutions.