Ok, took a look at the files. Something really strange is Happening, I can’t explain.
This “trim with regions” Fails nearly everywhere, and how the bottom part gets trimmed and not the top part, I can’t explain. So I thought, il try it with “trim with breps”, but as soon I try to extrude or whatever with your curves, it’s invalid. In GH it’s not calledd invalid, but as soon I bake them, or try “trim with breps” It doesnt’ works.
Tried it with 3 different methods, but it always Fails.
Also Curve/Curve Intersection Fails on your boundary curves and the rectangles to trim.
2012_01_02_contour_re.gh (87.3 KB)
May @DavidRutten can have a look, because it Looks like a bug for me.
But here’s the modified example script of bowerbird.
There you can also now modify the angle with a slider. And it creates you a solid version for renderings.
This won’t sound really professional, but just move your Roof a bit up, or extrude it in z, till your waffle isn’t visible anymore. Or move your waffle a bit down. Nobody will notice 
Ok, this gave me a guilty conscience. So I also made one with the Surface curvature. But not cut out, it’s just for Renderings.
