Right, and then they ignore the .tex sources, including formatting, and reset the whole thing in some weird proprietary system anyway, making half of the compliance to formatting that I did completely pointless. (And in the resetting, they introduce a few new errors into the references for good measure.)

Yeah, the whole problem is that traditional publishing is designed around creating the best experience for publishers, not for authors or audiences.

The reference formatting thing is just one of the ways they make it obnoxious for authors (it would be better for authors if you could just send them a list of DOIs and their computers should make it look the way journal style dictates — ELife does this). Idiosyncratic rules about the naming of sections or formatting of methods or supplementary material make transferring article between journals (even at the same publisher) unnecessarily tedious.

From the audience perspective, nobody wants to vault over the paywall to click on the link to click on the link to get the pdf that displays in a pane of the browser window. Nobody wants an enhanced pdf, whatever that is. I don’t want to see a pop up with the articles you think I should read next because they happen to share a single word in the title. I just want to click a link in pubmed or google scholar and go direct to the pdf. A few months back someone posted an enhanced google scholar that just linked directly to the PDFs from sci-hub. The user experience was so good that it really highlighted how obnoxiously bad publisher sites are.