I wonder if he was talking about the Registration Confirmation for DNN.
This can, of course, be avoided if you don't require your users to have a login. Then they would only get the one email from the cart, and nothing else.
If you want your users to create an account before they purchase, then they will get two emails; one from DNN confirming their registration, and one from the cart.
Of course, on their NEXT order, assuming they are logged in, they would only get one from the cart.