They say "These are are broadly applicable solutions for general problems that arise in enterprise software and productivity web app design. They are not web site patterns, which have already been cataloged and explored quite thoroughly*."

You say desktop and web apps are not the same. Sure, but the question is whether their logical UI differences are determined more by their webiness/desktopness or by the fact that most desktop apps are enterprise/productivity apps whilst the majority of web apps is not.