Something that's lost in all of this: What exactly is a second headquarters anyway, and what purpose does it serve?
In reading some of the Seattleish forums, you get the sense that Amazon is doing this because they want the option to be able to leave Seattle at the very least. Probably more scaling back. But when you own or lease 40% of the Class A space there it's not something you can get rid of so easily.
Getting all those tax incentives is a nice perk of course.