Great write-up so far, Foodchain.

Just tried this with 2 friends and it worked well (didn't crash), until acquiring Madora- then I got the "Each player must have a main character assigned" error, and that window would not close.

However, my friends were able to control their assigned characters just fine, but I couldn't move because of the Character Assignment screen stuck in my face.

Also to note-
Trying to start a game from character creation with 3 people made the 'Accept' button stay on 'Waiting...' forever. Only starts with up to 2 people, and more can join in after the game begins.

There is another meta.lsx file located in the unpacked Shared folder. So i figured I'd try what you applied to the Main folder- edit the numPlayers value up to 4, and put it in a new directory:
"Steam\SteamApps\common\Divinity Original Sin Enhanced Edition\Data\Mods\Shared\meta.lsx"

Didn't fix the Main character assignment issue. Probably useless information, but hope this helps! If only we can find a way to move past that error... Maybe adjust party member companions to be 'Main' players?