September concludes that there was never supposed to be a war between the two universes so thus there was a timeline where he never interrupted Walternate. He says that he went there to watch the moment when Walternate found the cure yet if it had always been a moment of distraction then nobody would have known it to be the moment the cure was discovered except our Walter (who never articulated it as far as I am aware) and September himself (who is unlikely to have told people from the past). There is also the moment where September erases his past self which causes Peter to drown in the lake (though I don't understand why he didn't erase his past self at the time of the Walternate interruption).
I think there was an original timeline where there were no Observers and now they live as an abstraction removed from the new history which exists. However I think you are right in your belief that they now exist in every timeline. Even in the final timeline where the Observers are never created the science team still exist - however when their mission concludes prior to 2015 they return to their now defunct future and disappear along with all the others.