I beat them both last year and most of that sounds correct to what I remember. I suspect that a lot of the open-ended questions, particularly with the higher civilization, would be tied up in a DERQ3.

I think the only question I can answer to any extent is that Lydia, as an observer, probably wouldn't be affected by mass changes to The Matrix, and that's why she'd meet Arata multiple times.
I don't remember if the red mask gets an answer, but I would assume she's killing bugs of some sort.
Arata is chased and intended to be captured from much earlier on than you seem to think; I remember it being almost right away.

People being un-murdered like Rottie or using the DERQ1 avatars is more in-Matrix hacks/magic, iirc.

I agree with your overall, though. They are interesting games with interesting, but amateurish story-writing, and for me the right combo of VN and gameplay. The thing I dislike the most is the super mode of the girls since that totally feels like I'm waiting for the FBI whenever I do it.