I didn’t really have a problem with the article. I wonder if the issue is that the article looks too much like the (false) claim that sales tax always works like your example, which is refuted by pointing out the exemptions, rather than the claim that the exemptions don’t always work.

I can imagine that pointing out some (hypothetical) tax where rates aren’t marginal could get a similar reaction here (ie lots of “OP doesn’t understand marginal tax rates, but that’s ok because lots of people are stupid,” rather than “oh dear, that’s not a very good tax system, I wonder how that flaw slipped through.”)