I’m not sure exactly what you are looking for, but If it’s aligning bones you can use snapping(Shift+Tab) and set it to vertex(Ctrl+Shift+Tab). If you want it to align it’s rotation as well, then you need to check align rotation to target(CTRL+Shift+Tab). You can also snap 3D cursor to places(Shift+S) then snap selected bones to the 3D cursor(Shift+S). You can also select multiple bones. Then snap to active bone[The last one selected with brighter outline](Shift+S->Selection to Active). This doesn’t rotate them to match, but you can use the copy to selected option in the n-Panel.
As for the Visual, this is how it appears in reference to the world/global origin. For example: If it’s parented then it’s transforms are in reference to the parents origin(Head on a bone).
