Hi,
It more about PR sculpting then stopping PR from flowing. Some pages simply don't need PR passed like contact, privacy policy type pages. The other reason its for siloing to prevent theme bleeding, and even though this can be achieved with sections, categories, articles and menu's, the problem happens when the same menu displays on the other silos.
Having the main nav with rel="nofollow" solves this, and making a manual footer nav, that is contained in an iframe (without sql queries etc), means that only one document contains the follow links, and its only a matter of getting external links to each silo/theme.
Does this make sense?
Cheers - Dallas