Eh I don't think you can classify surviving as winning. Mutants had sporadic moments of expansion and thriving but in the end were always brought down low and pushed to the brink of extinction.Technicaly the "homo novissima" didn't made the mutants extinct. Though defeating them and putting their remnants in cages as "zoological excibit" is not much better either. Which is however still more than what could be said about the base humans in that timeline. Who actualy did become extinct, when the homo novissima replaced them and mutants as default form of humanity (or technicaly ended it).
Ironicaly it means that those caged mutants were basicly the last survivors of the original humanity, as they were still at their core regular humans who just had randomized super powers placed on top of that by their X-gene. While homo novissima were so heavily augmented with super powers at their core that they have much more of a reason to see themself as not being humans anymore but something beyond them.
Also calling them the "final stage of the human-machine alliance against mutans" might not be entirely correct. Since their very existence has made humanity extinct (except for the caged mutants as mentioned above) and because they kept the machines as servants rather than as equal partners.
Homo novissima aren't slaves to machines like the humans shown in X2 (Life 9), instead they ensured machines to be their servants, because they no longer need them for their powers and protection anymore. Having powers beyond those of machines in their biological bodies.
The Librarian even pointed out that what the Sentinels did was not to help humanity win against mutants, but just delay them long enough for humanity to turn to and refine the technology of genetic modifications to create "homo novissima".
Basicly the conflict with the mutants, which the mutants kept on not losing, made humans so desperate that they turned to changing themself so heavily that they were no longer humans.
Which is actualy quite interesting to think about. "Sentinels bought us years. Nimrods bought us decades." The librarian basicly says that mutants always survived or even won against all the machines thrown at them by the regular humans. It was only the creation of a form of humanity which is better than the mutants thanks to not having an "x-factor" for their super powers anymore, which allowed someone to defeat mutants. But at that point the normal humans ceased to exist too.
It's also noteworthy that the Sentinels and Nimrods were shown vaporizing human figures and standing on piles of human skulls. While the context might suggest they are all mutant victims, what is ultimately shown is them killing humans on the order of other humans.
As weird as it might sound. What we saw wasn't that "mutants always lose", the opposite actualy. X3/Life 6 indicates that mutants always won, over and over, until someone better than them showed up. But at that point the original humans were long gone and mutants had taken their place as the power wise "inferior" form of humanity.
And this all gets me worried about what Magneto's and Xavier's in their current state might have in mind as endgame for mutantkind.
Because what they might actualy plan is not to prevent "homo novissima" from existing, but to create them first only replacing digital and metal based machinery with mutant power and organic material based machinery. They've seen a stronger form of humanity than mutants are. So what if they didn't saw a horror in them, but a beauty to be achieved?
The scene in Powers of X #6 where Xavier and Magneto talked with Moira X, seems to set them up with having made their own plans, that might even go contrary to what she desires.
The five allready act like a manufactory. Forge allready creates machinery (including humanoid war machines resembling sentinels) from Krakoa's bio-mass. Mutants allready desire having their powers altered via rebirth. The Chimeras are basicly proto-homo-novissima (people created with purpose given powers).
The elements are all there.
During House of X/Powers of Ten and it's early promotion imagines, some have speculated that Xavier might have been replaced by The Maker from the ultimate universe, because of the similar shaped Cerebro.
But that's obviously not the case. However this does not free him from potentialy being set up as being on the path of becomming a counterpart to him.
Ultimately what might be at stake here is not just mutantkinds survival, but that of humanity in either natural form (powered or not) and not because of the dangers of technology, but because of the conflict between the two parts of humanity leads to their mutual destruction via a replacement.
If that's the path Hickman has in mind, it will be quite interesting to see who wises up to it. Perhaps Moira X herself?