I generally don't do PDF conversions, but I have one book that I've done it with. I started it months ago, did at least two passes on it. The first conversion was unbelievably scrambled. It has pull quotes, and some text decoration.
I'm doing a basic reformat now, effectively a third pass, and I'm still finding errors and awkwardness. Probably looking at something like 12 to 14 hours total, maybe more.
The book is probably worth it. Most aren't, especially if there's another format available. The major argument for PDFs is that they are viewable as the designer intended, without regard to hardware, available fonts, etc. This particular PDF was pretty ugly, so no loss there -- in fact the version I'm developing is far more attractive.
I expect that publishers prefer PDF in part because it is so dang difficult to convert. I also think that sometimes they intentionally obfuscate the layout as a form of security.
m a r