You probably mean literally every native system. Because it's not like native toolkits didn't exist on the same systems as HTML+CSS.
> a flexible layout system that can
There's significantly more that's required of UI than just layout. And HTML+CSS are horrendously bad for anything beyond a static page of text with images.
For layouts, I've used various toolkits including Qt, Java AWT and SWING, and Visual Basic way back when. Creating a GUI that scales gracefully on these, in my experience, is time consuming and highly difficult. Most everyone favors static layouts because of the challenges. Learning responsive design on a web page takes a bit of time but it has the tools to reasonably manage a variety of layouts on a wide range of screens.
I would even accept an individual native system's layout manager as a counter argument of something that is at least competitive. It really isn't an easy problem.
These facts are obvious to anyone who has seen anything else besides just HTML+CSS.
Adding a simple box shadow on an element will trigger reflow in most browser engines [1] Efficiently animating anything that as much as breathes at layout is impossible. Efficiently displaying anything beyond a few hundred elements on a page? Equally impossible (and there are no virtual lists on the web).
But the actual argument is this: given "the most advanced and powerful layout system in the world that has no parallels anywhere else, it's so unique", why is it that most CSS frameworks struggle to implement anything beyond the most basic of controls (buttons, links, may be tabs)?
> Creating a GUI that scales gracefully on these, in my experience, is time consuming and highly difficult.
Ah yes. "Scales". Because this is the area that only HTML and CSS have to deal with. Because, you know, resizing windows didn't ever exist since the earliest days of GUIs.
However, being able to work at different sizes isn't what "scaling a GUI" means, or should mean. Desktop apps have been able to work at different sizes for close to 40 years now.
I mean, there ARE downsides to using web tech, but as a flexible layout system that can gracefully describe very large ranges of targets I have not found it's equal.