Hi Jirka,
Hello Sean,
Second, as regards the problem you mention, yes, you are correct. The link mentioned is not generated through the JoomSEF module. To change this behaviour, some changes in Joomla core files would be needed.
We may apply a patch which will solve this quite soon, but it is not priority #1 for us right now, so please be patient.
is this still on the list of future changes? My main entry page can be reached as our-url as well as the our-url/index.php. From seo point of view duplicate content is not good. I have worked around this using the robots.txt blocking the our-url/index.php to stop robots indexing the our-url/index.php page.