Why PDFs in the first place? They're hard to write, hard to format, hard to generate, and they do no good at all to anyone. HTML is better read, smaller, faster, has more formatting options, and can have all contained in a single file. Seriously, stop creating PDFs.
I agree that maybe layouting based on physical paper is maybe not ultimately necessary, but it gives the reader a familiar structure. The way the advertised web site is transferring the papers into a long scrolling list of text ... I find it rather disorienting and unstructured. Text that is split up into "pages" (whatever size they are in the end) somehow helps break up the reading flow.
In the end it remains to be shown that the gain from having academic papers not typeset in PDF outweighs the hassle of having to deal with non-standardized ways of rendering properly formatted text on websites (thinks like MathJax etc. do not support everything that is available in full LaTeX etc.).