Many hours later... I know a ton more than I did about writing shaders. However, I'm stuck sooner than I planned to be.
Before worrying about the actual clipping areas, I wanted to just have a working shader that would allow a 3D mesh to show over NGUI with a single transparency value (e.g. whole mesh is Alpha=0.2). I cannot get this to work properly though after numerous ideas. The problem is that NGUI is either covering my mesh OR my mesh is on top but also cutting a hole in NGUI and allowing stuff below it to show through. I'm using a modified version of the "Unlit Transparent 3" shader of NGUI.
I've tried using "Offset -2, -2", "Offset 1, -100", "Offset -1, 100", and various other offsets (no luck). I've also tried using different render queues (like "Transparent+1", "Transparent-1"). The approach I'd like to try next is doing "UsePass "Mobile/Diffuse/FORWARD" followed by a generic pass for clipping that works for ANY shader that was called via UsePass. Does this sound viable?
Haven't given up but this is definitely frustrating. Google searches are helping, but tips here will be appreciated too.