Can I "drush rsync" with "chown @ destination"?
If you do not tell rsync to preserve the uid, then it will create all transferred files under the ownership of the user that you connected as.  The key, then, is to make sure that you put 'remote-user' =&gt; 'bob' in the site alias for your destination site.

The rsync flags I use to achieve this are -rlptz.  So, in my drushrc.php, I have:

$command_specific['rsync'] = array('mode' =&gt; 'rlptz');


See also:

http://drupal.org/node/1169776#comment-4612944

http://drupal.org/node/1343892

Supporting rsync modules in Drush would be awkward. If you want to use modules, it's probably best to call rsync directly.  e.g.:

rsync -av --rsh=ssh drush dd @siteA root@siteB.loc::SiteB

You would need to configure your SiteB module to point to the Site B Drupal root anyway, so it seems like there is little value to tying this to a site alias.