Having a DOM, having structure, having a hypermedium is a source of immense potential & power. For both developer, but also, capitally & uniquely, for users too.
This longer top-commemt talks some to why documents, why hypermedia is enriching: https://news.ycombinator.com/item?id=31373988
For documents, yes. For apps those are obstacles. Apps just need something to draw on.
That said I disagree with the idea that using the DOM is bad - I suspect it's cumbersome to you mainly because you're not used to it. The number one benefit of the DOM is that user-facing controls are largely consistent. If I want the user to type text into a text box, I can just use a browser-defined element, and the user will be able to interact with that exactly as they expect. I don't need to reimplement the whole text input and display process, because it already exists in the platform. The same goes for all sorts of controls and interactions, from zooming to select boxes.
Moreover, assuming this DOM is built up in a way where the semantics are embedded in the elements themselves, then it can also be used in different ways. One user might use their browser to render the DOM into something that can see on their screen, while another might use their browser to read the element contents aloud. One person might use their mouse to interact with the system while another might use their keyboard. Accessibility is built into every application built using the DOM - it may not be ideally presented in some situations, and it's still possible to get things wrong, but by default a blind user will at least have a chance of using the system. In contrast, a canvas-based application will need to reimplement accessibility from the ground up (usually in the form of a secondary hidden DOM tree).
HTML is a document format at its heart and there's no getting around that, but <object> is/was a nice escape hatch.
JS is unfit for the task. It is a dynamic scripting language introduced by Netscape for the only purpose of adding a bit of interactivity to web pages, not to create large apps.
.NET and Java are much better for the task. The VMs support better languages with better libraries and more sane ecosystems. And the performance would be much better than that of JS.
And is easier to write an application using Xamarin or MAUI then using React.
When you write Java or .NET apps you write to target a computer which is a much better model for the apps then Web.
With "app languages" you can write apps better, faster while having better performance and more capabilities than using dynamic scripting languages like Javascript, Lua or Python.
Operating systems and browsers are apps too. And we don't use Javascript to write them.
You can write anything in any Turing complete language. But you'll be a fool if you attempt it for anything but fun.
That said, some of your statements seem to be simply false. Javascript engines are at this point about as heavily optimised as Java and .NET runtimes, and a quick scan through a few benchmark sights seems to indicate that, with a few exceptions, the two perform similarly well. Certainly, there is no guarantee that a naïve implementation in Java will necessarily be faster than a similar one in Javascript, in the way one night expect with e.g. C and Python.
Moreover, JavaScript is regularly used in all sorts of applications and systems - Gnome, for example, uses JavaScript for various plugins and utilities, an increasing number of applications are written using Electron or other webview-based technologies, even browsers use JavaScript for a significant number of controls (e.g. the devtools for most browsers are written in JavaScript). So clearly a lot of people see value in writing all sorts of applications in JavaScript.
The rest of your complaints seem to be largely your opinion - again, perfectly valid, but other people will have different opinions, and so the value proposition for JavaScript will be different for them. For example, for me, building something in React is a cinch, whereas Xamarin would take a lot more work. And the ecosystem of JavaScript may not be perfect, but it's very well oriented towards building front-end apps, something that isn't as true of Java.
