The nature of the elements of the set does not matter, since the existence of a choice function on the set A guarantees the existence of a choice function on the set B as soon as there is a bijection between A and B. Thus, no matters how counter-intuitive or unnatural one finds the elements of a set, or whether they model physical reality, what matters for the axiom of choice is whether one can construct a bijection with a set that has a known choice function.
By the way, it is worth keeping in mind how Gödel proved the consistency of the axiom of choice. Roughly speaking, the steps are: start with a model of ZF, build from it an inner model where all sets are definable (in a sense) in terms of ordinals, that model (called the "constructible universe") satisfies the axiom of choice. In other words, the axiom of choice holds as soon as you assume that all sets are constructible.
OK, but how are you going to construct a bijection from an arbitrary infinite set of undefinable numbers onto a set with a choice function without the AoC?
By the way, it is worth keeping in mind how Gödel proved the consistency of the axiom of choice. Roughly speaking, the steps are: start with a model of ZF, build from it an inner model where all sets are definable (in a sense) in terms of ordinals, that model (called the "constructible universe") satisfies the axiom of choice. In other words, the axiom of choice holds as soon as you assume that all sets are constructible.