Lots of times the people on HN advocating for native ui toolkits just have fond memories of a form builder on Windows 95 when you didn't have to worry about all these different screen sizes and stuff.
What desktop apps are people using today that still have static sizes (outside of dialog/info boxes)?
HTML-based applications however also introduced a number of new metaphors and patterns such as the page paradigm that, while originally reminiscent of printed pages, is different from anything both in the physical world and within native desktop applications.
Typography and information hierarchy are other aspects that usually can't be implemented as easily or as flexibly with native UI kits as with HTML-based approaches.