We're getting this from the 3.5.6 version (the version we are using right now).
My college told me that this line:
o.worldPos = TRANSFORM_TEX(v.vertex.xy, _MainTex);
was already into the original AlphaClip shader (the original file we modified). It allows to get the coordinate on the UIPanel (if I'm right, I'm not a shader guy...).
Then the other line is used to be able to scale the alpha with the size of the Panel.
If you still can't figure out how's working with the latest version of NGUI, we will tomorrow try into an empty project with the latest version of NGUI those changes. If we manage to do it I'll post here the solution.