I think they mean it as more of a "hey, might as well, you never know" thing than anything else -- and it can't hurt -- but yeah, it gives folks the wrong idea about general Mac OS best-practice maintenance requirements. If someone hadn't updated their OS in a very long time and is the type to install all sorts of junk from all over, I certainly wouldn't advise against repairing permissions. But I also wouldn't have it in my step-by-step list.
I think the most-important step to highlight is quitting all running apps and not toying around with the system during the update, especially not Apple apps (!). And for folks who leave their Macs running for days & weeks at a time, a fresh reboot first wouldn't hurt to flush things out (but not necessary). My own personal paranoia is still using the combo updaters just in case, but in general that isn't usually necessary anymore for most folks. I always like to have a copy of the full combo update installer for corporate rollout anyways, so the extra download time doesn't phase me, as it may some.
