Hi Bee,
The fact that the Y-Axis of a Bone is along its length is not very surprising; it’s the same as the Y-Axis of an Edge (Mesh in Edit Mode).
An Armature comes in, with its Axes aligned to the World, so nothing special there either.
The rest is a ‘mystery’ (or probably, just a choice).
Why is a single Bone standing, when Adding an Armature? (Because its common use is for characters?)
Why is its Head down and its Tail up? (Because the system was made by an Australian?)