Let me throw an idea out at you. While I have not done a ton of full size maps I often encounter depth issues when doing my top down objects. I think that you could indicate height on areas that need it by using tapered buttresses. The top would match the texture of the higher elevation, and the stone texture and width of the buttress would scale down as it moved away from the structure. This should help establish the roofless area as being higher and make for less confusion to the viewer.
I did something similar with cliffs under this rope bridge object one of my site contributors submitted.
Private use only. Do not redistribute.
I might be able to mock something up over the weekend, if you would like to see an example.
Hope this helps.