Question Why the transform of rootBone changes the axes of SkinnedMesh(vertices)?

I found it recently that assigning rootBones with different rotation values will change the axes of skinned mesh on the renderer, hence the vertice of the mesh will have different x,y,z directions, which could possibly cause problems if we need to make use of those directions. Any idea why is that and how to deal with it?

This issue occurs when doing both manually assignment and scripting.