Sure, they're technically building on top of the native UI frameworks, but only by completely ignoring all of their functionality.
https://developer.apple.com/library/archive/documentation/Co...
UIKit/AppKit is layered on top of Core Animation which is layered on top of Metal. Skia, the 2D graphics library that Chrome's rendering engine uses, is built on top of Metal (or at least transitioning to Metal from OpenGL on macOS).
So browsers have the same flexibility in principle as native UI toolkits and they are just as close to the metal. There is no inherent disadvantage. But flexibility is a double edged sword. It includes the ability to diverge from the platform look & feel. So that's where the debate has been raging on for decades.
In terms of performance I think any debate about optimisation of UI stacks pales in comparison to the question of where the data lives, who generates it, and how it gets to the CPU/GPU for processing and display.
If people want to use web technologies on the desktop, there is Electron.
The converse is not true.
Quite a few of the ‘cross platform’ toolkits work this way.