Some webmasters want their sites indexed under the www version of their domain; others want their sites indexed without the www. Which do you prefer? Now you can tell us and we'll do our best to do what you like when crawling and indexing your site. Note that it might take some time for changes to be reflected in our index, but if you notice that your site is currently indexed using both versions of your domain, tell us your preference.

http://googlewebmastercentral.blogspot.com/2006/08/more-webmaster-tools.html

But that's just for their crawl right? I mean what happens with PageRank? When people link to www. and non-www., PR is split, theoretically. I can't imagine this Sitemaps feature would bundle the PR (if it is indeed split) 'cause that would favor Sitemaps users over non-Sitemaps users. And Google can't do that unless they risk lowering the quality of their SERPs.

Since they don't crawl the others they probably wont rank it. You're right if people link to the other one, it'll create issues.

One can still set mod_rewrite redirection (301) in .htaccess