Here are some thoughts:
1. Can you change the render queue for STM and your glass shader for this situation?
2. Is a rendertexture acceptable for this? e.g. point a camera at an STM object, output rendertexture to surface?
Besides that, I do wonder if I could modify the output to go directly to a texture... it would be a pretty big rework though and not technically a mesh anymore, but I do like the potential of this, even if it's just skipping the rendertexture step. Not sure if I could get it running any more eddicient than that does anyhow off the top of my head! (on the fly texture creation vs. extra camera in scene)