All of the diagrams are of a cross-section of the middle of an onion. You know, it being round and all, it naively makes a lot of sense to assume that's going to be ok as a model for the entire onion.

But ... I find myself curious ... if the solution is to cut to an angle below the onion, and the article did point out that a few pieces along the bottom would be mismatched ... It seems that we are overlooking the top and bottom of the onion where sections are going to get some really weird looking cuts.

They say, "This is an onion. (Well, a simplified cross-section of one.)"
... No. No that is not an onion. Its not that they've chosen an easy problem, but the approximation used here is not an onion.