Although Apple wasn't explicit, I believe only the $30 upgrade from Snow Leopard to Lion is exclusive to the App Store.
The App Store doesn't exist in Leopard and Tiger, so Apple will probably release a full price DVD set for $180 that includes Lion, iWork, and iLife.
Not exactly great, but it is an alternative if you don't want to download from the Mac Store. Keep in mind, prior to Snow Leopard the OS X upgrades were $130 anyway.