Ok, here's what's going on (for others who run into this) - the S&H is "preliminary" until you log in for the checkout. Once you log in and get to the final checkout screen, it knows whether or not to charge the S&H. In my case, when I got to the final Confirmation page, it dropped the additional S&H and only charged me the bare $20.
I assume it works this way to allow customers who pre-ordered digital-only versions to easily upgrade to the LE (which is a physical product and therefore requires a S&H charge).
