Hi
I am not very familiar with mapping buildings. The osm inspector (areas) picked up the problems because you used a multipolygon relation which appears ok now .
I expect that an easier way to map complex buildings is to use a type=building instead of type=multipolygon. I think the way to construct the various parts of the building allows for overlapping ways. You need one way encompassing the whole building and then all the parts fit inside, each with their own individual tags. All of these polygons, including the encompassing one and any holes (inner) go in as members of the relation.
I have not made myself familiar with building relations so I could be a bit mistaken.
But I think using multipolygon relations for mapping complex buildings is fine too.
I guess each is done with a differing method. 
Which method you use is probably just a personal preference I guess and one may be more suitable certain types of building.