It’s true that you can route through highway=pedestrian areas. However, if there is a building in this area (as is the case here, and a pretty big too as it’s the world’s third largest mosque…) you can not route through it. So that would exactly be an argument to draw the building on top of the area, no?

You also say that buildings should not be rendered over regular linear roads, because of a building that is near the road overpaints part of the road. So what about buildings that completely cover parts of a road? Let me give you 2 examples, located just next to my office building, so I can assure you that the building is covering the road in it’s entirety. There is the parking on the ground level, and the building covering that parking with it’s first floor. I can send you a picture if needed.
The cover tag would not work, as it’s not a cover but an actual building that is on top of the road.

[openstreetmap.org/?lat=51.676823&lon=5.334613&zoom=18&layers=B000FTF Second building in the lower right]
[openstreetmap.org/?lat=51.678081&lon=5.329665&zoom=18&layers=B000FTF Below the Provinciehuis]

Once again, the representation of those 2 areas made by Osmarender is more correct, as the road is not appearing to be on top of the building.

So if you let me voice my concern, this definitely seems like a bug in Mapnik as we need to add a multipolygon for the rendering to be done as expected. This contradicts the idea of not tagging for renderers (or renderer in this case, as Osmarender has got it right)