It's not exactly entirely doomed; John and Roxy (and Jasprose and the migrant Davesprite?) are from that timeline and they are now alpha. General!Tavros is from that timeline, and in the scheme of fighting LE, he is now also alpha. John couldn't get his powers without that timeline, Roxy made the matriorb because she had practice with John, and Tavros finally got fed up enough to gather the army on his own because of those events.
I kinda think the retcon powers are a loophole that Paradox Space is cultivating to get around LE's tinkering with things, by giving John the same ability to tinker with things, then healing itself into the alpha timeline where this group of players has to cauterize the wounds LE is making into a bundle of doomed timelines, then allowing the players to escape that bundle.
Doing so seems like a larger-scale version of Aranea's original plan... taking the useful parts of doomed timelines and nurturing them into a strong, combined alpha. She made it all about her, which was incorrect and cost her everything. The rest, including the dreambubble army, are fighting for the right cause, so they are relevant and alpha to the grand plot of the comic. This ties in with what Dirk said about no version of any character being less important than any other... Dave wouldn't have been angry enough to call out Dirk if Bro hadn't been such an ass raising him, so Bro continued to be an important plot mover long after his death. Dreambubble army presumably works the same way... you have a huge pile of pretty badass players, many of whom have godtier-level abilities, that have been cultivated through hardship and soul-searching to fight this fight on their terms. All of them are fighting LE... all of them from all those "doomed" timelines are relevant and important. As the comic goes, they are alpha and critical to the final victory over LE as far as we know.
I'm going to take a break from shitposting textwalls now.