Well, if they DO merge the codebase, and wp.org is run on wp code anyway, then both instances are right. Also, check this tweet out:

@janeforshort has clarified that WPMU and WP will be merged to offer an option for multiple blogs in WordPress. No timeline as of yet.
— Matt Martz (@sivel) June 2, 2009
No source, but this guy says Jane says it's the first option, the merging of the codebase.