I guess I disagree. I think a good author can make a good book no matter what. I know what you mean by the publisher and staff. They might restrict the author in some ways, and probably even "break" the book, like you stated.
I think though, if the author is good, he can work around that. Overall, to me, if the author can explain the material well, I'm satisfied. Even if it has mistakes, I'll excuse that if he has a web site for errata, for which most do. Let me give you an example. I despise the O'Reilly format. When I open up one of the books, the layout reminds me of man pages (linux documentation). It just gives a very dry appearance. This is not the author's fault, it's the standard layout all O'Reilly authors have to follow. But then when I read "Programming ColdFusion," by Rob Brooks-Bilson, I forgot about the way it was layed out by O'Reilly because the author was good enough to explain the material in a way that kept me interested.
I'm speaking from experience by the way. I buy an average of two books a week and own several online books from Sams, QUE, Wrox, O'Reilly, New Riders, McGraw Hill, Osborne, and Coriolis, and Friends of Ed. I already know the layout of each publisher. I'm not going to tell you which one is the best because again, in my opinion, it all depends on the author. You can however distinguish them on length, but I'm not going to do that because that also depends on the reader.