This was tested on a clean 5.2011 install with MatchOrder set to uri.

Basicly, RemoveSiteAccessIfDefaultAccess setting in site.ini is by default turned off (set to disabled) when you install eZ Publish and it is ignored when generating URLs.

Loading the site without the siteaccess name in URL generates links to other content nodes without siteaccess name in the URL. Forexample (default siteaccess is eng, the other one is cro):

http://my.site.com - will NOT generate siteaccess name in URLs - Not correct
http://my.site.com/eng - will generate siteaccess name in URLs - Correct
http://my.site.com/cro - will generate siteaccess name in URLs - Correct

This poses a problem when upgrading old installations, which was my case recently. I upgraded a site from 3.8.6 and all URLs lost siteaccess name in them.