Just to contribute to this thread, I remember pre-ordering Skyrim and picking it up on Day 1 only to find that the disc's installer pointed me directly to Steam to enter the code I was given on the box. I... remember not being very pleased with that as I didn't pre-order the CE or anything like that. However, something like that could work with this game nicely.

Truth be told, this very same thing could be done. Replace the Heavensward Disc and activation key with a Steam code.