Morrison went overboard in relation to his feelings about 9/11 and terrorism. Militant Magneto historically acts and behaves more like the leader of a rogue state not a terror group. However, that issue was very locked in early 2000s post 9/11 politics with Lorna taking the view of the Arab street vs that of the US. It led to a powerful confrontation that I would say without a doubt still stands as Lorna's best single issue.
I do believe Magneto lost too much of his edge in subsequent years and feel he is far better off kept in a broad framework where he is an X-Men foil but will certainly work with them for the betterment of mutants. The X-Men came closer to his old 90s ideology, and he moved closer to their ideology so there wasn't much day light. I actually felt both moves by the X-Men and Magneto created real problems for Lorna and her story compounded by them forgetting Genosha existed for her, but that is a digression.
In terms of this space arc it does look like it could take place pre-Judgement Day. We will know soon enough though I hope it does take place in that timeframe as it avoids obvious storytelling problems for her story.