There is a closing div in intranet-bottom.inc, the related opening div is usually added by the different template. Since it's at the top of the include file it does not make much sense to have it here, better to not add confusion to the templates and let them close it from there.
From IRC oleonard> Joubu: Re: Bug 30707, I know it was my decision ages ago but I don't remember the reason. It may not have even been a good one at the time!