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Just for the record, Atomic-X is already shown to be weaker than Alien X in the fight against Maltruant. Malturant's attacks can at the very least get a reaction out of Atomic-X, sending him flying and inflicting pain. Alien X takes a device at least strong enough to destroy the universe point blank without budging. Biomnitrix fusions are understood as a 50/50 DNA mixture of species, like a more stable version of Ben's hybrid aliens in the OS. You can't apply some sort of universal constant with regards to how strong a fusion alien will be when you're mixing DNA. Presumably Atomic-X is somewhere above Atomix and below Alien X in power along with some of Alien X's reality bending and the proficiency with nuclear power. Going back to Maltruant again, Atomic-X displayed none of the reality warping he could have to stop Maltruant then and there if he possessed reality manipulation to a similar degree as or even greater than a Celestialsapien.
The reason Ben 10K would use Atomic-X instead of Alien X, besides the fact that alien fusions were his entire gimmick, is that Alien X is ultimately an unreliable transformation which could trap him for all eternity. In Omniverse Ben can have them loan him control, but this is never confirmed to be a permanent deal. And if we aren't taking creator statements from showrunners at the time into account I'm not sure we can say that it's even possible for his Biomnitrix to be used separately to turn him into Alien X anyways.
The reason Ben 10K would use Atomic-X instead of Alien X, besides the fact that alien fusions were his entire gimmick, is that Alien X is ultimately an unreliable transformation which could trap him for all eternity. In Omniverse Ben can have them loan him control, but this is never confirmed to be a permanent deal. And if we aren't taking creator statements from showrunners at the time into account I'm not sure we can say that it's even possible for his Biomnitrix to be used separately to turn him into Alien X anyways.