If I start Blender in factory default mode, delete the original block and add a bone, the bone's axes (in pose mode) are not the same as the world axes. Y is where world Z is pointing, and Z is -Y. Why is that? Is there a way to override it?

When I import meshes to an application of my own, they will be oriented in X/Y/Z just as shown in Blender. But when I apply the bones position from a pose mode the whole model will be transformed (with the switch between Y and Z). As I have some problems interpreting the data from Blender, this initial transformation makes it much harder to analyze.