In UnityCustomRenderTexture.cginc, notice that in line 210 TEXCOORD0 is float2, but should be float3 in order to work with 3D textures:

struct v2f_init_customrendertexture
{
float4 vertex : SV_POSITION;
float2 texcoord : TEXCOORD0;
float3 direction : TEXCOORD1;
};

Z coordinate gets tossed in line 219:

v2f_init_customrendertexture InitCustomRenderTextureVertexShader (appdata_init_customrendertexture v)
{
v2f_init_customrendertexture o;
o.vertex = UnityObjectToClipPos(v.vertex);
o.texcoord = float3(v.texcoord.xy, CustomRenderTexture3DTexcoordW);
o.direction = CustomRenderTextureComputeCubeDirection(v.texcoord.xy);
return o;
}