Being overly fixated on the JSA, I went back over the scenes and switching around of Superman and them as reboots and recons shuffled their histories. I find the lack of mention of different Earths interesting. The original JSA was shown to want to get Superman (an Honorary member) in the first scene. This is followed up by a JSA who did not know who Superman was (the post-Crisis JSA). Superman's appearance in 1955 was meant to signify Earth One and future scenes reflect the changing post-Crisis combined Earth. And the 31st Century Legion appearance ignores the time-shuffling of that franchise being locked 1,000 years after the present year.
The only connecting factor I think I get is the focus on the primary Earth DC was using at the time. What Manhattan saw as a sudden disappearance of Superman in 1940 was something we knew to be a combination of multiple Earths and a reshuffling of the timeline. Is there a reason this was ignored? Now, I realize that an academic look at what Earth when would appeal to many of us on these boards, but to the readers of Doomsday Clock or even evergreen readers years in the future, maybe not.
I suspect there's a reasoning to Manhattan's odd focus. Or at least I hope so. If this is the resolution to the missing years and a supposed "fix" of continuity questions, the explicit spelling out of the situation has some meaning.