Sorry to report that the further explanation doesn’t clarify your issue much more.
I note that the geometry in you sample is not grouped and I wonder if this is why elements are being left out when you transform them. In the attached I have “grouped” all the geometry which then allows it to be moved as one item…rotating to get your boards level and further rotated for another view.
Again. The axes shown in the main window exist to orient the world’s coordinates, it does not influence or dictate the center of any rotation. The point of rotation is dictated by where you place the rotation tool, this can be arbitrary or locked to certain axes by using the cursor keys.
