Also, Genesis can not update .htaccess because...?
Because it is a theme and themes do not do that.
For example, you said that Genesis looks at the generated permalink - could you explain what it then does? A 301 redirect, or... ?
No redirects. It looks at the code and see the label "canonical".
These forums were CLOSED to new posts on November 19th, 2012. New forums are here: http://www.studiopress.com/forums/
and you will need to SIGN UP AGAIN.
If you need assitance with setting up your theme, go to http://my.studiopress.com/
and read the SETUP links or the TUTORIALS link on the side tab.
If you need Account Assistance
, file a help desk ticket at the same location.