While I can see that linked table of contents can be of use in a book where people might want to jump around among the chapters, I read mainly fiction and I couldn't care less about a table of contents -- I start reading at the beginning and place bookmarks so I can resume reading wherever I wish.
I don't particularly like indented paragraphs -- I prefer the blank space between paragraphs, so I'm not particularly thrilled with the feedbooks format. Your custom settings allow a great deal of customization, which is wonderful and people can get the font size they want with the margins they find most satisfactory, but you don't give the option for those of us who might want the extra space between paragraphs.
I don't know why it is but perhaps I've just read too many PG texts, with electronic book readers I prefer the extra space between paragraphs whereas with printed books I don't have a problem with indented text -- perhaps its because with printed text I have no options and can't change things.
In any event, the Feedbooks format is wonderful for those who like it, but the bebooks format is great for people who prefer it instead.
I wouldn't say one is well-formatted and one is not very well formatted -- I'd rather just consider it that one is well-formatted for people who like that format and the other is well-formatted for people who prefer that format.
That's why I thought I would share this new source for PDF files of the same ebooks everybody keeps re-hashing in slightly different formats. It might be better for some who want PDF ebooks in that particular format.
If people don't like it, they're certainly not forced to download any, but the more sources more of us learn about the better, in my opinion.