I think people forget that the work that goes into a pdf is often more than the printed work.
If the pdf is multilayered and fully bookmarked then more will have been done work wise and the people who do this work need paying too.
I think the Mongoose model of book + pdf for the same cost as just the printed book is fair. Having the pdf by itself cost almost as much as the book is also fair.
Except that you're ignoring the realities of the publisihing business...
The MSRP is typically 4× the cost to distributor, and half cost to retailer. Assuming that they're losing 40%, to DTRPG, and that the extra time prepping for PDF costs as much as per copy printing, then 42% (0.25/0.6) is plenty to maintain parity.
Layers and such are a standard element in most publishing software; if they're using actual page layout software (most likely Adobe inDesign, but there are other options, such as Scribus) the layers being accessible for turn off is pretty easy - and keeping things on the correct layers is just good design practice.
Internal links can be autogenerated, tho' it's not recommended; having added links to several books for my own use, it's non-trivial. (using just Acrobat X and an unlocked PDF, creating navigation ("Structure") links to chapter headings takes about 30 minutes for a typical 200pg book; to subheadings about 4 hours. Adding the structure links to the TOC was about half an hour. This was while only minimally familiar with Acrobat X.
So, about a day's labor.... but, having worked with Pagemaker, Scribus, and one other commerc DTP program, I'll point out that they generate the structure database automatically; including the structure tree is a single click. Adding internal links for the TOC is likewise minimal - a few minutes. And the PDF for the printer is, aside from resolution settings, able to be the same layout files. Changing the resolution from 2400 DPI (which is what my local printer wanted) to 150 (which is what we put on the website in the late 90's, when I was doing publication work as part of my day job) takes pressing Command-P a second time, changing the DPI in the output, and changing the filename.
As for the price charged the distributor, that's inclusive of printing. Which, based upon things said by Pinnacle Entertainment, John Wick, Margaret Weiss, RPG Pundit, and a few others in the OSR world, a typical small press company is marking the physical up 10% to 30% over cost to their warehouse. Smaller runs, higher percentage...
John Wick noted that he saw more money per unit selling PDF at $5 than selling the dead tree... I asked when
Houses of the Blooded was new... I never bought the dead tree on that one. IIRC,
Blood and Honor... $15 dead tree; $5 in PDF.