I've never actually questioned the why, so maybe you could shine some light... why are they usually published as PDFs?
This probably evokes some kind of sense of authenticity. Like some physical paper document it has exactly one appearance.
I don't know of any more convenient way to directly attach my thoughts to a specific portion of text. (If there is, I'd genuinely like to know).
And it even works well across multiple devices: I have a folder on my PC that's synced with my phone via syncthing containing mostly PDFs (savend web pages, papers, books, ..) and the annotations I make in those PDFs on my phone are directly available on my PC ... all without using some cloud bullsh*.
Regarding your question, I'd say that it is a natural continuation of centuries long tradition of writing on the actual paper. The invention of TeX actually made it easier to produce more papers, then came PDF, and you could produce virtual papers. Also science journals pretty much have monopoly on scientific knowledge distribution, and they are mostly paper too
My guess is it's largely for historical reasons. At the time most venues were organized PDF was probably the best (or only) mechanism for sharing documents for print distribution.
But we think it's time to change that :).
PDF is the only widely supported format can guarantee accurate reprint.
HTML for text.
SVGs for diagrams.
Equations can be exported as images if needed.
If all goes well we won't need this software anymore. In a best case scenario the publishers start accepting HTML, and gone are the days of having to convert PDFs to something better...!
Page anchors can be used for navigating between sections. We present a table of contents that makes this easy. For instance:
https://papertohtml.org/paper?id=6f9fc51102cf49bff4f4e2b3367...
It would be great if you could add some basic CSS rules for print? Right now navigation elements are needlessly repeated on each page, obscuring the content.
Also, you forgot to include bold and italics webfonts, so you have faux-styles for all headings and emphasis.
You know what, they are.
I like print format for reading purposes, even if it's on my epaper tablet. The other day when I took a train for 8 hours, I printed out several papers to read on my b&w laserjet. And it's more difficult to read diagrams these days because people make them all in colour, sometimes in ways that are very difficult to read when it's converted to b&w.
I find it a real tragedy that all these efforts to turn papers into dynamic content, which I wholeheartedly applaud, ignore the still very relevant use case of printing. Every preview mechanism for camera-ready papers should include a b&w print-preview mode.
The other advantage of PDF is that "page count" still means something. There's a reason journals limit page count, and it's not because it adds a few kbs to the download. It's because long-winded papers that don't get to the point need editing.
Here's the output of this tool on this PDF - https://arxiv.org/pdf/1909.00031.pdf - content is preserved, but text is readable: https://imgur.com/a/EPCaWxP