I agree with you from a technical standpoint — something created for displaying and navigating between documents is being misused for distributing apps.

At the same time though none other model affords the same distribution, write once run everywhere. No other distribution platform can compete. And users have become accustomed to the web being apps as well as documents. In fact, many have become accustomed to more or less treating their web browser as an OS (or more realistically, not giving the distinction any thought).

Maybe an interesting way forward could be a web model specifically for apps, which of course many would say would be WebAssembly. The HTML/CSS/JS combo has been remarkably successful and resilient though, so I'm not convinced it will be dethroned easily.