I know that's the actual publication history of things. My point is that Johns showed the JSA roster sans Superman in conjunction with the 1956 Superman rather than the 1986 Superman. And I think he did that deliberately, not just because it would be harder to explain the team's absence during the Silver Age version of the Metaverse but also because part of his premise is that Jon removing the JSA was an act that knocked an essential foundation out from under the Metaverse. You don't get that if there's an iteration in the revision history where there was no JSA but the rest of the Metaverse carried on without any problem.

So I think this is a retcon of the meta-history. It's not without precedent: basically, the whole “Perpetua and her three sons” storyline in Justice League is a massive retcon of the very beginning of the meta-history.