Unity Custom CutOut Shader

Hey guys!

I've been searching Google, Unity forums and Unity Answers, all looking for a simple solution to my problem.

I downloaded the latest source files for built in shaders.

I then adapted the Cutout Diffuse/Spec/Normal/NormSpec shaders to use a custom texture for my alpha. This is primarily for carpet edges, fade out effects, etc.

The problem I've come across is that for lightmapping, it seems to always want to use the Alpha Channel of "_MainTex", regardless of how I have set up the surface shader.

In a previous thread I read that downloading the Extended Lightmapper plugin would help, but I didn't see any settings that would help with this case.

So is this to do with Unity's internal workings, or is it because of the fallback shader handling the shadow casting.

If it's the latter, how do I fix this?

Here's the Cutout Diffuse Shader. You can see how little of a change I made.

 Shader "Fade/Diffuse"
 {
     Properties
     {
         _Color ("Main Color", Color) = (1,1,1,1)
         _MainTex ("Base (RGB) Trans (A)", 2D) = "white" {}
         _AlphaTex ("Alpha", 2D) = "white" {}
         _Cutoff ("Alpha cutoff", Range(0,1)) = 0.5
     }
 
     SubShader
     {
         Tags {"Queue"="AlphaTest" "IgnoreProjector"="True" "RenderType"="TransparentCutout"}
         LOD 300
         
         CGPROGRAM
         #pragma surface surf Lambert alphatest:_Cutoff
 
         sampler2D _MainTex;
         sampler2D _AlphaTex;
         fixed4 _Color;
 
         struct Input
         {
             float2 uv_MainTex;
             float2 uv_AlphaTex;
         };
 
         void surf (Input IN, inout SurfaceOutput o)
         {
             fixed4 MAIN = tex2D(_MainTex, IN.uv_MainTex) * _Color;
             fixed4 ALPHA = tex2D(_AlphaTex, IN.uv_AlphaTex);
             o.Albedo = MAIN.rgb;
             o.Alpha = ALPHA;
         }
         ENDCG
     }
 
     FallBack "Transparent/Cutout/Diffuse"
 }

Thanks!