If we ever get the opening tool to work with roofs this should be easy.
For 3D purposes you could form a Morph and subtract it from the elements you want to remove using SEO. The Morph needs to be assigned a strong Building Material with a high Intersection Priority Value. Place the morph on a layer that will normally be hidden with its own unique Intersection Priority. Unfortunately SEOs won't show in 2D plans.
What I ended up doing is redefining my composite roof, I just added air space between the layers I wanted to have the timber. Originally I drew to roofing materials on top of each other with timber in between. That allowed me to use the skylight tool so that I could place a skylight that went through the entire roof...
I ended up having to manipulate the top-most layer so laying my skylight for some reason only could cut through the bottom composite roof and not the topmost metal roofing. I watched the "how to cut a hole in a complex roof" video and basically used the roof tool again, to make the actual hole the size I needed.