If you’ve ever tried to switch the rendering mode of a material in Unity 5.0 on run time, you might have run into some issues with it not updating properly. This is what I thought would do the trick just fine (sidenote: 0 = Opaque, 1 = Cutout, 2 = Fade, 3 = Transparent), but it doesn’t actually update anything (in my case, I wanted to fade out an object).

mat.SetFloat("_Mode", 3);

If you look in the GUI code for the shader (Editor/StandardShaderGUI.cs) you can find the following code that handles the changing of rendering modes, and will show everything you need to solve this.

public static void SetupMaterialWithBlendMode(Material material, BlendMode blendMode)
{
	switch (blendMode)
	{
		case BlendMode.Opaque:
			material.SetInt("_SrcBlend", (int)UnityEngine.Rendering.BlendMode.One);
			material.SetInt("_DstBlend", (int)UnityEngine.Rendering.BlendMode.Zero);
			material.SetInt("_ZWrite", 1);
			material.DisableKeyword("_ALPHATEST_ON");
			material.DisableKeyword("_ALPHABLEND_ON");
			material.DisableKeyword("_ALPHAPREMULTIPLY_ON");
			material.renderQueue = -1;
			break;
		case BlendMode.Cutout:
			material.SetInt("_SrcBlend", (int)UnityEngine.Rendering.BlendMode.One);
			material.SetInt("_DstBlend", (int)UnityEngine.Rendering.BlendMode.Zero);
			material.SetInt("_ZWrite", 1);
			material.EnableKeyword("_ALPHATEST_ON");
			material.DisableKeyword("_ALPHABLEND_ON");
			material.DisableKeyword("_ALPHAPREMULTIPLY_ON");
			material.renderQueue = 2450;
			break;
		case BlendMode.Fade:
			material.SetInt("_SrcBlend", (int)UnityEngine.Rendering.BlendMode.SrcAlpha);
			material.SetInt("_DstBlend", (int)UnityEngine.Rendering.BlendMode.OneMinusSrcAlpha);
			material.SetInt("_ZWrite", 0);
			material.DisableKeyword("_ALPHATEST_ON");
			material.EnableKeyword("_ALPHABLEND_ON");
			material.DisableKeyword("_ALPHAPREMULTIPLY_ON");
			material.renderQueue = 3000;
			break;
		case BlendMode.Transparent:
			material.SetInt("_SrcBlend", (int)UnityEngine.Rendering.BlendMode.One);
			material.SetInt("_DstBlend", (int)UnityEngine.Rendering.BlendMode.OneMinusSrcAlpha);
			material.SetInt("_ZWrite", 0);
			material.DisableKeyword("_ALPHATEST_ON");
			material.DisableKeyword("_ALPHABLEND_ON");
			material.EnableKeyword("_ALPHAPREMULTIPLY_ON");
			material.renderQueue = 3000;
			break;
	}
}

As you can see, you need to set more variables in order to swap the rendering mode in real-time, so to switch an object from Opaque to Transparent you will have to do the following:

mat.SetFloat("_Mode", 3);
mat.SetInt("_SrcBlend", (int)UnityEngine.Rendering.BlendMode.One);
mat.SetInt("_DstBlend", (int)UnityEngine.Rendering.BlendMode.OneMinusSrcAlpha);
mat.SetInt("_ZWrite", 0);
mat.DisableKeyword("_ALPHATEST_ON");
mat.DisableKeyword("_ALPHABLEND_ON");
mat.EnableKeyword("_ALPHAPREMULTIPLY_ON");
mat.renderQueue = 3000;