I was looking through the threads about this and only found threads with no replies in them and they were old threads.

So, for whatever reason the game does not allow hi res 1920x1080. So what is the best setting to use for a monitor that does allow this?

I do not want to use fan made patches BTW. Why hasn't this game been patched by GOG for higher resolution?

You inadvertently answered your own question. Its because GOG doesn't want to use fan-made patches (with some exceptions).

If you want to play with high and/or widescreen resolutions, the "Deus Exe" launcher is your first and only stop.

Link: http://kentie.net/article/dxguide/ (two pages)

Take your time and read this article, ignore the mod suggestions (though the Direct3D 10 renderer is very good!) and get the game running well without messing with the art assets or gameplay. If Ion Storm had anticipated 1920x1080 the game would look like this.