Interesting that the USB stick version is so much more, I assume it's really only for those upgrading from pre 10.6, so it's similar to the cost of Snow Leopard + Lion + cost of media
More likely it's a signal that the USB option is not the preferred upgrade mechanism. Apple wants to push every possible user to the App Store, and it's only extenuating circumstances that are forcing them to offer the USB stick at all.
Or those with high bandwidth costs. While $40 might be more expensive than a single download, if you know multiple Mac users in an area with small caps it might make sense to split one of these.
I'm curious how (/if) the license ties in to the App store. Hopefully they don't make you tie it to a single account once your computer is running.
edit: thank you