Apart from the false dichotomy (the fact that HTML is a document format and that its structure plays an important role in browser layout are both true), I totally agree with you. HTML was indeed never meant for that but it was often sold as such by evangelists, hence the last remark (I wasn't complaining about HTML).
You are complaining about the wrong thing.
> Despite the popular claim to the contrary, HTML was always part of the presentation layer.
Not at all. It is document format. Designs that do not respect that doesn't change it's intrinsic nature.
This is like complaining that a shoe isn't a very good mallet.