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That's right, he didn't mention it, even that being one of the greatest mistakes in Linuxland.
He didn't even mention that vim uses different keybindings than emacs or how Konqueror renders some webpages differently from Firefox! Well shit, this article is worthless!
1. Adding a side bookmark on a KDE Open/Save dialog box doesn't put that same bookmark in GTK dialog box and vice-versa
Valid point. I don't know if fd.o addresses that somewhere.
2. Gnome programs have their confirmation dialogs with switched buttons (the No/Yes question in Gnome dialogs)
Well, cry me a river, people actually have to READ before the hit a button? Not to mention that "yes" and "no" is not really wanted according to the HIG (or so I heard). If it really bothers you that much, go install one of the GoneME patches that "fix" this "issue". And don't you dare start with "but the average user does not want to install patches, he just wants his buttons in the right order". The average user is a braindead idiot who shouldn't be allowed to walk, else he could fall and break his neck.
3. Changing UI settings in KDE doesn't change them in GTK and vice-versa
True, but there are some people working on that. Look at Metatheme for example (I do not have a link handy, but it is somewhere on themes.freshmeat.net).
4. It really looks bad
Depends. It can, but does not have to.