I ran a few more tests. The only point I would like to address with regard to the setup script is that you have defined the vertices of the facets in a clockwise direction. It should be defined in counter-clockwise manner (looking from outside the object) for a facet and clockwise direction for a hole in the facet. But making that change just shifts the rectangular protusion from left to right.
I checked the index with different types of mesh and different levels of accuracy but nothing seems to help. I also checked the rendering of the object in wireframe form and I do not see any issue with the visualization of the object itself.
I will pose this to the larger team including the R&D by the end of the day just to make sure that we haven't made any mistake with the setup. If it turns out to be a bug, I will submit a bug report and we can discuss if there are any alternatives.