Since I was specifically asked, yes, the OP covers my main arguments quite nicely. But in essence, I would argue the web is content-oriented, and the PDF is not.

For example,

1. The web is a medium where you cannot (within reason) exercise too much control over the design of things. You lay out general guidelines that tell the browser how to render whatever content is thrown at it. I won't pretend this gets us predictable design, but at least it's uniform, which is good for human consumption.

2. The web is a medium that lends itself to structural document construction in such a way that it is easy to use and reuse the content in ways not anticipated. This is good for machine consumption, which in turn empowers the human.

These arguments may seem philosophical, but they do have real-world effects. Once I managed to explain it in ways the customer understood, they were always eager to be of assistance in the endeavour.

As long as we're speaking in idealistic terms I pretty much agree with you but when you compare websites and PDFs that exist in practice it tells a different story.

Zooming PDFs on mobile can be a pain but it's certainly less of a pain than using some fixed width site from the early 2000s with a jQuery menu you can only operate with a mouse and links so small that a mouse would fat finger them.

Machine consumption of the documents is one of those benefits that sounds cool but really just boils down to SEO because very few other things are going to be scraping your site. Certainly worth something but it's usually not high on the priority list for governments and search bots scrape PDFs anyway.

I think the main point in favor of the web is that you can have multiple presentation layers for the same underlying content and you can improve presentation independently of content. Not necessarily that it's reusable because that's just templates and a style guide but that you can backport all your fixes.