Yeah, basically the idea seems to be that once year of the villain started the timeline became fractured and it operated under Hyper Time rules, and basically each book sort of became its own timeline, but they were still affected by each other.
But once the League truly unifies all time and makes "everything" matter, the 60 year timeline will take hold, everyone will age, and events will be reshuffled according to the new timeline. So for now, Bendis is able to use the Kents alive and well and in the present, but once the 60 year timeline hits they'll both likely be dead again anyway. And the original members of Young Justice will have aged into their late 20s early 30s.
And as for Doomsday Clock, DiDio already flat out confirms that Doomsday Clock will be part of continuity, but it won't have happened the way we read it.
But in the most basic sense, JL issue #39 is the true start of 5G and the 60 year timeline.