So there I am... Toying with Arcanum one Thursday afternoon, and I accidentally throw something at my teammate, Virgil. He get's pissed and starts attacking me, but I, obviously, being stronger, slaughter him. I just felt like messing around that day and so I cast a Ressurect spell on him and quickly Dominate his Will. I look him in inventory thinking "This will be funny, I'll remove the Dominate Will spell, and remove his equipment whilst still in the inventory menu. I do just that and besides Virgil attacking me. He just stands there, after I removed Dominate Will. I then talk to him, and he says. "I can't believe it...! I mean, you... And then the zeppelin...! And the fire...! And the altar says that...! Yadda yadda yadda. Strange, eh? Any other glitches related to this?
Aside from the last bit, it might not be a glitch. If you go off and start hiting your teammates, they'll get pissed off and then they'll either leave or fight you. Often times you can bribe them with stuff (Magnus with snuff for instance) and they'll calm down. Never tried the combo your talking about, but my advice is reload a saved game before its to late. Errors have a way of propagating and then coming back to haunt you later in the game.
I've visited the Iron Clan and Virgil somehow tripped whatever triggers Magnus' dialogue and as he didn't have a specific dialogue he reverted back to the Crash Site conversation.
So... Virgil was saying what Magnus is supposed to say? Or it was the conversation when Virgil was talking about Magnus.
Now, my dear friends, that's called a bug. But, how's the conversation between Loghair and Magnus supposed to end in there? I always come to a point when you can choose a further "listen", but they say nothing more and the conversation is cut. I know they must've more to say to each other.
With Loghair and Magnus in the Iron Clan, yes, Magnus does become the leader of the Iron Clan. Then the dialog between you and Magus becomes whether or not Magnus adventures on with you.