Why was the Emperor looking for the magus? Which magus was he even talking about?
The stone guardian's master (a man long dead). Technically, it's not the Emperor who's looking for him but the voice in his head, the one he acquired during the failed ritual.
Also I know the story is not the focus of this game but is there any chance we could get an epilogue screen explaining what happened to everyone after escaping? I assume Marcus got killed since Cado is still in control of the guild in AoD but I'm curious.
We'll consider it.
1. How did Gaelius manage to get word of an uprising, assemble a century, and have them march to the mine so quickly?
Talk to the Praefectus. You can ask him the same question and he says: "They aren’t here for you. There was a ... disturbance here a while back. It was reported to House Aurelian as per protocol." When you dig deeper, he says: "You don’t understand. The nature of this disturbance... It can be anyone and you can’t tell who until it’s too late. They won’t take any chances."
2. Assuming Dellar isn't one of the anonymous convicts that follow you, how did he escape?
He escaped before the events of the game (without making as much noise as you did). He spent ten years there, worked his way up to be close to the fort, then waited for the right opportunity to slip away and climb down the mountain.