That's usually just how I do crossovers in general, when sending people from one universe to another. Read any of my crossover stories where its one person going to another universe (mainly Taylor from Worm, admittedly) and it's pretty much always a permanent stay. Queen Weaver, The Bug Bender, Skitter's New Team, The God of Death. The main issue isn't a lack of attachment usually, rather its that traveling universes isn't easy and thus going home is usually impossible or at least very difficult regardless of whether a person wants to go back or not. Because that would almost always be where the crossover ends. It wouldn't usually make sense to continue the story after that point since they'd never really have much reason to go back unless they had some attachment to the other universe that made them want to go back.
I could see an argument that Ben would go back due to his heroic nature and wanting to fix the Warhammer universe after spending enough time there and realizing how bad it is. But the premise of this story isn't "what if the Warhammer universe merged with Ben 10's universe" it's "what if Ben 10 got sent to Warhammer 40k". Azmuth, Professor Paradox, and the Plumbers could probably fix up Warhammer in a few years if they really wanted to. The Tyranids? Capture them and put them in their own little ecosystem where they aren't an existential threat. Chaos? Go back in time and stop the War in Heaven from happening by curing the Necron's cancer. The Imperium? Have an organization like the plumbers work with the now saved Old Ones and Golden Age humanity to ensure the rebellion of the Men of Iron never happens and malevolent alien species can't prey on mankind. And ensure the Enslaver Plague gets stopped. Not to mention if the Celestialsapiens intervene.
If Ben gets 100% access to his own universe at any point, the entire setting of Warhammer gets nullified and it just becomes an extension of Ben 10's universe with minimal effort. Thus the story ends. Unless Ben fixes everything on his own, in which case the story ends regardless and him returning becomes moot.
Both of these options require the death of all life. If the Tyranids consume everything, everyone dies. If the Necrons kill everyone, everyone dies. The only way the Chaos Gods get starved is in the "Rocks fall, everyone dies." scenarios. Which Ben won't be inclined to use because he's not just going to decide to exterminate all life to just starve chaos to death.
He could help the Eldar make Ynnead, which could kill Slaanesh or maybe imprison it like the Elves did in Warhammer Fantasy, but that still leaves three other Chaos Gods, The Emperor who could become The Dark King, Vashtorr the Arkifane who could become a fifth Chaos God, and possibly Malice if we consider him canon.
Chaos isn't the kind of saturday morning cartoon villain you can just defeat and call it a day. It's the collective unconscious of every living thing in the universe corrupted by the intense negative emotions and massive trauma generated by the biggest war in the history of the universe, in which the most powerful things in the modern setting are like toys in comparison.
Khorne is the psychic manifestation of rage, hatred, war, murder, and bloodshed. As long as those exist, so will he. Those things still exist in Ben 10 so I don't see how Ben with his limited arsenal of aliens could fix that.
Nurgle is the psychic manifestation of death, disease, rot, stagnation, entropy, and destruction. All of which still exist in Ben 10.
Tzeentch is the psychic manifestation of change, evolution, mutation, intrigue, ambition, knowledge, sorcery, destiny. lies. and trickery.
Slaanesh is the psychic manifestation of pleasure, passion, excess, pain, and perfection. It's also the only one with a specific weakness in the Eldar and Ynnead.
Chaos cannot be truly defeated as it is currently. Only fought against. The only way to stop it is by altering history so it never came into existence in the first place.
This is before the fall of Cadia.
Probably about as strong as the Emperor before his interment upon the Golden Throne, but since Slaanesh is after them they wouldn't be able to employ their full power. Thus making them on the level of Eldrad Ulthran or Malcador.
So basically the average Naruto fanfiction then. Yeah, this story isn't going to be like that.
