That's a cool idea Synaesthesia and would work pretty well. BerserK, one other thing to keep in mind is that in some versions of max RTT will fubar the padding if you have more than one map output in RTT. So bake the maps one at a time if the padding ever goes wonky. Diffuse only, or AO only, but don't add multiple map…
What is in the render window isn't correct and should always be ignored. It is a full render including the scene lighting (even scenes with no lighting still have the default light(s) behind the viewport camera). But if you don't want the actual shadow map, then you should render a diffuse map with lights and shadows…