I believe you’re confusing a few different stages in the book creation process. Also, the submission you’re responding to was about web publishing, not print.

I publish printed books for a living. I’ve been involved in the design, editing, and marketing of printed books for 20 years.

Unless the person you speak of self-publishes, he doesn’t pay anything for the lay-out of the book. If he does self-publish, and he has retained someone to make it into a half-decent book, then yes, that person should advise him about logical structure and appearance (depending on what that person is paid to do.) And yes, hopefully, the person he pays to help him does know more than him about creating books and shouldn’t be afraid to give his professional opinion.

Remember, a manuscript does not a book make. Experienced authors know this and value publishers.

I respect your experience in publishing, but I think it misses my point. It may be that you work with different genres. My point was that for many authors, particularly authors on the high end of the fiction market, appearance does matter to them. These people love books, not just the words but the physical feel and appearance. They have opinions about the physical form their book takes. Are they wrong?

I've helped a few authors get set up with their own websites, and the same concerns translated. They cared very much about how the site appeared, and had intelligent opinions about why that was the case. They weren't web ingenues -- they'd been reading other author blogs for years. Why would their concern with the appearance of the written word change when that word was online?

I can't name names, but these authors were far from self-publishing. They had substantial contracts from major houses. Their books were all covered in the NYTRB. The publisher of course paid for one lay-out of the book, but it was not customary to cover three. That's why the author used his personal funds -- for the extra two lay-outs.

No one's saying authors shouldn't care about the appearance of their book, they're saying it should be decoupled from the production of the manuscript. You can productively worry about the appearance after you get the "nice list of words, with chapters" aspect of the manuscript down; that's the logical structure, and, obviously, the hard part. The point is that you don't need a perfect WYSIWYG editor for the manuscript.

For my inner web designer this reads like "I want to see my blog in three different themes". Cost: A few minutes.