He has used it as an element in numerous other stories over the years too - there was a Final Crisis primer he wrote featuring The Spectre which used the same beginning-of-time visual as seen in Justice League this month. Earlier than this The Anti-Monitor was a major element in The Sinestro Wars. Later his Justice Society work owed much to it in the latter years of his run.
As an additional thought on JL #40 - It does occur to me that if Metron has total recall of all the Crises and revisions over the years then logically so would the Anti-Monitor... I doubt Johns is going anywhere with all of this, but it goes to cement the now undeniable deep interest he has in the original Crisis.
Maybe we can get back the COIE in this upcoming war between two of them, and get back the real DCU again
When Darkseid and AM go to war, would beings such as Guardians and others stay on the sidelines or not?