I believe the policy you're linking to isn't longer in use, or is a
kind of double. Since the creation of the
http://www.mediawiki.org/wiki/Manual:$wgForeignFileRepos plugin every
mediawiki installetion can use Commons, and as far as I know its
supported by the Foundation.
I checked the Foundation site but couldn't find a policy against
hotlinking, so I don't think the Foundation doesn't want stuff
hotlinked, and if the do the could do it very easy with a server
configuration.
But again, why should the MediaWiki core supports Commons if the
Foundations doesn't support hot linking?