Bahikka, the bosses typically opens up military tech, so after X minutes after that specific tech is available, the boss will spawn, regardless of your presence. There is a percentage chance for it to start moving towards "something" after Y minutes, based on difficulty.
Only way you can control this, is to unlock specific military techs when all of you are online, focusing on the boss.
This said, I'm confident that you should try it out, and see if it fits your playstyle. I have had a couple of always on servers, myself, in SE, Py, Nullius, with varying success, I would never consider do it with this mod, as you are so behind, if you don't get the missions done. Some tweaks on evolution by time and pollution map settings can mitigate this, though, pretty sure you can find a nice balance for a 24/7 server, too.
My experience: The hardest biter battles, the most ruined base, the weirdest factory structure, the most distinct battlefield... MSI II delivers something unique.