Waverider(aka. "The Seer of Hypertime"): "I can sense a web of possible timelineS... Past and future... Enmeshing him in a tangle of alternate realitIES.": http://i.imgur.com/uyDHQ6U.jpg
*Confirmation that Dominus created/merged multiple universeS...
Superman: "Why the FOUR realitIES for me? Was it all in my mind? What was Dominus after?"
Kismet: "It was NO hallucination. [Dominus] warped ALL of reality so he could draw me from hiding.": http://i.imgur.com/Bdzlo3P.jpg
And Rip Hunter, who knows more about the inner-workings of DC cosmology than ANYONE, referred to Kismet as the "Illuminator of realitIES": http://i.imgur.com/wL9ZuQW.jpg
Heck, even Kismet's official bio gives her multiversal status: http://i.imgur.com/eyPRoJC.jpg "Base of Operations: ALL known realitIES"
*And again: Dominus >> Kismet... He trounces Jamie without much issue, tbh.
The story continues in Adventures of Superman #561 which centers around the hunt for Kismet (after she fled from Dominus who merged the four realities just before his confrontation with her). Waverider converses Superman about the events which happened in Superman #138, but it's revealed that Waverider is actually Dominus:
We also have Waverider telling Superman that the meeting between himself and superman in the previous issue was not actually him. Superman deduces that it was Dominus and goes with Waverider to search for Kismet. Reality starts to warp and it turns out that this Waverider is Dominus as well, fooling Superman for the second time.
And after that directly Dominus forces the multiverse madness upon Superman after which the real waverider along with linear men show up (they never did previously, it was all Dominus).
So no, those issues weren't one big fat warp. They were chronological events taking place after the four realities were merged. Quite clearly, i might add. So im not sure where you got that they were all part of those four alternate realities.
Not sure what's your point here though, but whatever.
The problem is that you didn't comprehend the story right. Personally, i legitimately dont give a shit if Superman has beaten a multiversal being or not.