It is a limitation. Anyone who's ever tried to read a PDF journal article on their phone has experienced it. (and don't even get me started on Unicode copy/paste...)

HTML can be styled in a fixed layout if desired, and reflowed by a reader mode if needed. PDF can't be styled in a responsive way, and there's no (easily accessible) reader mode equivalent for PDFs.

HTML is a far better document format than PDF.

> there's no (easily accessible) reader mode equivalent for PDFs.

It’s called Liquid Mode in Reader, and it is, in fact, easily accessible.

> HTML is a far better document format than PDF.

HTML is better for some things, PDF for others. That's why PDF is widely used on the web when HTML is available.

Liquid mode only works we for a subset of PDF files. And sometimes it doesn't work at all.

Reader mode only works well for a subset of HTML files, too.

Yes, of course.

A significant advantage of the two column journal format (although still they end up feeling pretty clunky on a phone).

True, but the rigid layout is what makes PDF unsuitable for some use cases. It’s main use is to represent a printed page of a very specific size. Anything outside that just requires too much flexibility.