Why did changing my shader's Render Queue affect the pivot point of my sprites?

I have been messing around with skewing vertex and uv map coordinates in a shader. I acheived the effect that I wanted but once I changed my render queue from Transparent to AlphaTest the pivot point behavior changed dramaticly. My transform matrix gives me completely different results. 1. Why is that? 2. Does the coordinate change between object and world space in different render queues? 3. If its not an object/world space issue, how do I fix it? Thank you!