Notice the gray margin outside the sheet, and the padding inside the sheet. The first one gives you a general frame of view, and also you don't want the document to use the whole screen width when using a 16:9 monitor or similar screen.
The padding is necessary because you don't want characters too close to a margin, else they look like they're escaping the sheet.
I haven't been able to replicate this setup with Calibre, FBReader or any other epub reader.
Fonts are another issue. Default fonts always suck. FBReader uses Dejavu Serif, that, in my opinion looks just bad. I changed it to Bitstream Charter, which looks decent, but then the line justification looked wrong, I changed that, and then paragraph margin looked wrong. There's a million little things that look horrible by default and you have to spend an hour per book setting up your reader so that it looks right.
I've tried generating PDFs with Calibre, the result: giant ugly fonts, zero sheet padding, nonsensical spacing, etc.
At some point you just give up and avoid epubs like the plague.
[#] The book is called Crypto 101, by lvh.
If anything, I think an HTML version that you can view right on the website would be the best format addition. It's always interesting to me when a website doesn't offer a browser-native document format as an option to view text.
I could spend the time trying to make them look right, but I don't want to spend my time that way. I prefer learning things that will give me more satisfaction per second spent.
I find any of them far superior to PDF.