I agree with you on every point here, John. Scholarly publication needs to take into cognizance that the world of web has grown so much and so fast that it has left the old safe world of paper based knowledge dissemination far behind. So, while we browse our smarphones and our browsers, we still read printed paper copies of our “papers” in double column serif fonts, and have to go back and forth between section in the paper, citation, and reference, and back with a highlighter or pencil in hand. Whereas, we could easily hyperlink to the particular reference and get the things done.
I also like your idea about standardisation. You have given an example of chemistry (very appropriate example), and this can be extended to other tools as well (say statistical data analysis software, or clinical instruments). In both counts of standardisation and hyperlinking, a web based “research publication” is superior to paper based ones. Then there is always printing for those interested. I tend to eschew paper based publications if I can. I consume or prefer to consume my reading on my kindle/phone/tablet/computer. It’s just getting better and better every passing day.