theGaVrA, did you ever find a solution to your problem?
I have the exact same problem as you, and I understand your explanation perfectly.
What I don't understand is why Brandon claims the behaviour is the same on 3.0 as 2.3. To my mind it is not the same, no matter what settings you use on 3.0. And my members are complaining the same.
What I would like is a list of new content the same as on 2.3. Namely:
List of all topics that have been active since last "mark all read" (not since "last session"), those that are unread have a little orange icon, those that are read have no orange icon but are still displayed.
It seems, however, that with 3.0 such a listing is impossible.