TerrainData terrainData = terrain.terrainData;
Texture2D holesMap = TexToTex2D(terrainData.holesTexture as RenderTexture, TextureFormat.R8);

byte[] pngholesData = holesMap.EncodeToPNG();
if (pngholesData != null)
{
    File.WriteAllBytes(path + "/" + holesMap.name + ".png", pngholesData);
}

private Texture2D TexToTex2D(RenderTexture texture, TextureFormat format)
{
    Texture2D texture2D = new Texture2D(texture.width, texture.height, format, false)
    {
        name = texture.name
    };

    RenderTexture currentRT = RenderTexture.active;

    RenderTexture renderTexture = new RenderTexture(texture.width, texture.height, 0, GraphicsFormat.R8_UNorm);

    RenderTexture.active = renderTexture;
    Graphics.Blit(texture, renderTexture);

    texture2D.ReadPixels(new Rect(0, 0, renderTexture.width, renderTexture.height), 0, 0);
    texture2D.Apply();

    RenderTexture.active = currentRT;

    renderTexture.Release();

    return texture2D;
}