I have not seen the tracking work yet since I just used the app - however, I viewed the source for my pages and the code is there.
If you host your site on your own domain, It does make it necessary to use an ftp app or some other tool to publish your site instead of publishing directly from iWeb. I think it would be a gret addition to the app to support sites hosted anywhere, but it is not a huge inconvenience to publish the site
to a local folder and then "upload" the pages from that folder to my hosting service.
MusicOnMainStreet about SEO Tool for iWeb