The footer include should be the last thing on your page before the closing tags...which include the table closing tag and the body closing tag. You have to have it before your table ends anyway.
I think they are trying to simplify the placement for people who have no knowledge of HTML...hey...we have struggled through AJ's template together...we are no longer novices
I think we have a long way to go to reach TechiGuy, James, and Lisa's levels...but we have definitely made some progress on our path of knowledge!
Anyway...I think really they are having you put it at the bottom just so it is easy to find. Technically I think it would work anywhere on your page.
As far as the optimization...they haven't won me over with that yet. Some of those links are still way out there and I don't know if they can optimize it to perfection yet. I think some of the clicks I get (and I am definitely getting clicks there) are from people who might think they are my links that will take you to other places in my site. That doesn't thrill me but I haven't taken them off yet.