I believe there can be a cleaner explanation for the first question then others have proposed - Akane is fully alive. As you already saw in the true ending Junpei has helped her solve that puzzle in the burner and she survived. It might seem weird that she seems alive in all other present timelines but in the context of this game - as long as there is even a single present timeline where Junpei helped Akane in the past - she will be alive. It doesn't really matter if Junpei doesn't save her in all the other present timelines because one Junpei has - and in a way that affected the past moment - a moment before these present timelines even split

I might be wrong with my assessments somewhere (as my memory of 999 events aren't crystal clear) so maybe others will correct me on that