I don't get it. Never heard of any layer limit in KS. As you see my old project above had so many layers, every part, one layer, all rendered KS. You can place them also manually on different layers. If you are talking of 5 different parts of the wall, this is not that many. Just grab the components with the same material manually and assign to a layer
Should be easy in keyshot 6 to assign materials to different surfaces of parts now. 'subpart'-selection should work now.
Personally i don't like keyshot for this kind of project since this can get tedious.
btw. there was a very informative series called Keyshot Master Series, watch this, totally in depth on workarounds in Keyshot 6, this one is on Material Control: