Every day now, you see the question
I just upgraded my account and blog to New Blogger. Where is my Layouts / my Labels / my link to Upgrade my template?
and you look at the blog URL (when it's included), and it's not yourblog.blogspot.com.
And the answer is always that, when you publish externally (aka FTP publishing), you don't get any of those features. New Blogger 2006 requires publishing to blogspot.com, for maximum benefit.