I've never tried summoning Hyborem or Basium in MP using the latest version of EitB, so I'm not certain what happens now, but at least in other versions of FFH you'll get a prompt asking if you want to take over the new civ, just like in SP. The AI will get a turn in first though before you're formally handed control, so from the player's perspective they lose a turn, and in the case of the Infernals the AI has a tendency to use that turn to do really stupid stuff, like upgrading your starting Manes into Scouts.
If a player doesn't care about switching civs, then the game will simply continue as normal, but with the addition of an AI player.
If a player doesn't care about switching civs, then the game will simply continue as normal, but with the addition of an AI player.