Is there a difference now? Websites in Safari ask me to pay with an Apple ID popup that takes my fingerprint and charges me exactly the same way apps do, I don't see any difference in how it appears or is handled.
I have to say I disagree there. "Our program for handling HTML+CSS content should handle HTML+CSS content stored in containers" is a much more reasonable idea than "Our program for opening containers should also handle whatever content is inside those containers." It's a common thing for programs to do. VLC plays videos in zip files and RetroArch plays games in zip files, for example.
And I don't think reading a book and browsing the web are fundamentally different activities. They're near-identical. The web was created as a way to access documents consisting of text, images, and links to other points within the current document or to other documents. A book is a document consisting of text, images, and links to other points within the current document (endnotes, footnotes, "see page X") or to other documents (references/citations). The UX and features you'd want for a book reader are the same you'd want for a browser's Reader Mode, as implemented by Edge, Firefox, and Safari. I don't see any difference between reading an ePub file and reading a long article on a website.