Think of the ichthyologists. I'm sure they like it when people call them ichthyologists, but most of the world has no idea what exactly that is and how it's different, so in the news we just call them scientists or biologists.
Personally, I don't find it offensive, but there are plenty of people who have had it applied to them offensively who could. It's still a charged word - give it another decade or two.
Back on topic: I still find both 'nerd' and 'geek' to be offensive. Although I don't find "geek chic" to be offensive... probably because it has never been associated negatively - it has always been a label for a particular style, which in itself carries no meaning.
I think the guideline might be based on that "geek" has historically been a negative label, except where applied internally (as many negative labels do). So when paired with a non-existent or neutral phrase, it takes negative connotations, while when paired with a positive phrase it becomes a new "thing", and no longer holds the negative slant.