Ben Traje,
Do you have a reason to use anything but the Z axis? If you look at the IK tag, if the Auto option is on, it aligns along the Z axis. But yes, any axis can be set. That would be one default, to point out that Z is preferred.
Example, for other alignments, as in none, going by the joints direction: Like with Maximo-rigs, where every axis in the T-Pose have 0º and can be reset quickly, even without the need to have been frozen before.
We could go deep into the rabbi-hole and explore the rotational hierarchy, finding out that the B axis is the last one which will be rotated until we see that someone even changed that default as well. This is my idea about, but I haven’t found that in any Cinema 4D (or so far I had access) in any other rigging source, so I can’t really quote anything here at all.
Joints can be aligned:
https://www.cineversity.com/vidplaytut/character_rigging_in_r12_aligning_joints
Cheers