<Snipped quote by Flamelord>
<Snipped quote by TheWindel>
But if it were like that, there should be witches around. And we should definitely be on the race against the doomsday clock 'cause if no one stops Walpurgis Nacht, the world would be reset again. You should remember that after Homura made her wish, she basically trapped the whole Earth on an endless one month time loop until she could save Madoka. Nevertheless, things play different in each iteration and the canon characters die in different ways always, in fact, as per Urobochi's own words, Sayaka is supposed to die even if no one else does (she absolutely never survives a reset because shes too idealistic).
In many ways, when you deal with a story based around time travelling and reality warping it doesn't make a difference if you're in an alternative timeline or on a prequel/sequel.
I had two thoughts. One, it's an alternate timeline, due to the fact that she reality jumps while going back in time, so therefore it wouldn't be unfeasible to find a timeline where these Primordial things exist rather than Witches. That would also explain the apparent lack of time stopping murderhobo killing the plot, because Homura doesn't exist here (yet). And it's not like time just stops after Homura hits her personal reset button. It goes on afterwards. Homura didn't trap the Earth in a time loop, she trapped herself. And it was reasonable, from my perspective, that this was one possible variation.
Alternatively, it was an actual sequel, with the Primordials being the results of (one of) Madoka's wishes rather than Wraiths. This was less likely though, since then Sayaka wouldn't be alive in the first place and Kyoko would be in Mitakihara. But it was a possibility, given the lack of any corruption cleaning mechanism, and it naturally going away on it's own.
So yeah, still not obvious to me until Windel basically said it.