Shapekey rotation

I’m using shapekeys for my animation and I know that shapekeys are linear transformation but I can’t understand why they wont work correctly if original mesh is rotated.

Here is how shapekey works with non-rotated mesh. Looks fine.

Here is how shapekey works when I rotate origianl mesh.

It looks nothing like it was in vertical position. Why? It is a linear transformation, shouldn’t it move vertices all same no matter how I rotate mesh? I am not even scaling it, just rotating it. Is there something I can do about it?