Why does changing a shader's Render Queue affect the pivot point of transform matrices?

I have been messing around with skewing vertex and uv map coordinates in a shader. I acheived the effect that I wanted but when I change the render queue from Transparent to AlphaTest It's as if the pivot point moves or the transform' matrix behavior changes. Basicly, the result of using my transform matrix changes and since im very new to unity I dont understand what is going on. I even read the manual. What is going? What did I miss? Thank you!