Honestly, that's just silly. If they'd use html instead of pdf, you'd still have the same content. pdf is a format. It has nothing to do with the content.
Didn't anyone notice that it's basically impossible to save an html page today and have it load and render correctly and offline tomorrow?
There are tools that try to fetch those links and update the HTML to point to the local copy. But those tools can only go so far. JS is allowed to fetch new files dynamically, and there's no reliable way to look at a piece of code and automatically figure out what it's going to fetch when you run it.
You've diverged from the context and are no longer doing an apples-to-apples comparison. The things you're describing are all opt-in and amount to having to deal with an adversarial input. There's nothing inherent to the medium that requires those things.
In other words, a person publishing a PDF is already abstaining from certain things. (Namely, the sorts of things you're bringing up that would make for a pathological case.) If the person who publishes a PDF does a straightforward translation into a web page, then you end up with something that doesn't exhibit any of the downsides you're discussing.
If I had an idea and wanted to communicate it, then I did so by recorded video, by live video, by blog post, by Twitter thread, and by HN comment, the same idea would be presented in very different ways.
In the same way, a writer who publishes something by HTML (blog post, etc.) will produce a very different document than if they intend to publish it by PDF (ebook, etc.). They tailor their message to the constraint and expectations of the medium.