Utilitarianism can argue for well-being as the goal via e.g. empathy, the golden rule, the veil of ignorance and peaceful coexistence. The basic idea is that I don't want to suffer, I don't want other people to make me suffer, I would like other people to help me not suffer, and I don't like seeing people suffer or living in a world where suffering is condoned. It seems most conducive to these desires for me to try to minimise the suffering of others, for the direct effect of them not suffering, and the indirect effect of them being more likely to oppose my suffering.
Meanwhile, a theist wouldn't just be tied to the axiom that "we ought to follow everything that God commands", but this would also include the claim that God exists, and the claim that God has commanded some specific things, and commonly also that you'll be tortured for all eternity if you don't follow those commands (although there's some conflict about whether following the commands even matters if you've already been forgiven, but that's a whole other discussion). These are not moral "oughts", but rather truth claims. And these are truth claims that aren't considered to be true by atheists (and by theists from other religions, or other denominations within the same religion).
* If it's true that not following those commands would lead to you being tortured for all eternity, then one can make a utilitarian argument for promoting the following of those commands (although following them yourself for that reason would be more egoist, i.e. just for your own benefit). But the sticking point, like I said above, is that many people don't consider that to be true.
Speaking more generally...
It's certainly someone's prerogative to request a justification for your moral goal, but it's also your prerogative to call that an axiom and say you have no justification.
Although if you have a moral goal that other people don't agree with, and you simply call that an axiom, don't be surprised if you're unable to convince anyone else of that goal, or if people call you immoral.
If you care about being a moral person, having your beliefs correspond to what's true, having a consistent worldview and being consistent in how you treat others, then you should care about having justifications for your positions. Calling something an "axiom" is functionally indistinguishable from simply saying you have no justification for it. For something to "truly" be an axiom, it would need to be impossible to justify it, which I'm not convinced is truly ever the case (but some people certainly think so... and justifying something to others is definitely different from justifying it to yourself). If you care about having justifications, calling something should be an axiom should be a last resort.
Does the exercise of challenging and requesting justification for ethical axioms presuppose that there is only one possible set of axioms that can be justified?
No, there doesn't just need to be a single moral goal. You just need to convince someone that some moral goal is something they should want. That doesn't preclude the existence of other moral goals.
How could axiomatic ethical disagreements be resolved in such a scenario?
If you treat moral goals as unjustified axioms, then you can't really resolve disagreements. But if you treat them as justified conclusions, then you can ask for that justification, and evaluate it with reason and evidence.