2 pages side-by-side on a sufficiently large screen looks great. I've only seen a few websites that flow text in columns and make graphics pleasant to interact with. Sure, many web browsers have reader mode but it's limited, clunky, and hard to configure.

Web designers have the idea that I want a big column of text running down the center and lots of whitespace to the sides, perhaps with sub-menus. This would look OK if I had my main monitor oriented vertically, but I don't and almost nobody does. As a result only about 50% of my screen space is working and I am constantly scrolling back and forth on long pages if I want to look back more than a paragraph or two.

I've developed a deep dislike of commercial graphic designers as a class of people because they took everything that was annoying about magazines and put it on steroids. Many graphic designers hate text and now we have a million interfaces that look superficially interesting but are deeply unpleasant to read.

The use case for 99% of pdfs is email transfer. They are absolutely superior to sending a clunky, bloated MS Word or CAD document. The web archive is just the final resting place in the process that made them.

Exactly.

With academic articles, I virtually never want to simply read them online.

I need to save them for future reference, read them later when I've set aside time, annotate them, refer back to my annotations four months later...

Arxiv (or JSTOR or wherever else) is just where you get the papers. It's not where most academics are going to be consuming them.

(For consumption, a full-size tablet like an iPad, with a stylus or Apple Pencil, is absolutely ideal.)

Same with electronic part datasheets. I need to be able to mark up and save datasheets along with the other documents which make up the design of a product.

Can I ask what app you use on your iPad for reading PDFs? I use Adobe reader which is pretty good on iOS, but I find Preview a better experience.

I have been maintaining a PDF library this way using GoodReader for about 10 years now. You can connect it to most cloud storage services or any SFTP or WebDAV server, and sync annotations with Acrobat, Preview, Okular, etc. on the desktop. I have still yet to find something this good for HTML or EPUB documents.