That'd make about as much sense as the DCFU's origin story...
Pandora: Barry Allen...I will use you to bring together again that which was once torn asunder...except for these two guys, one of whom is dead, who I'll put on ice for 1000 years.
Actually it might make perfect sense. Since the JL3K title started they have been deliberately "loose" with DCU history. They've said repeatedly that historical facts from the 21st century are sketchy due to a "Great Disaster" that occurred at some point after "our" time. The Great Disaster, if taken literally, is from the Silver Age Kamandi stories, right ?
They know that Barry Allen was the Flash but they thought he was red head. That wouldn't make sense in the New52 since Wally is now a black guy.
There has been no mention of Superman and Wonder Woman previously being in a relationship as in they are in the New52. In fact JL3K Diana has been sure that never happened.
So it may be possible that Giffen planned all along that this title was set in the future of the old DCU.