I think the distribution center was owned indirectly, through some sort of holding company; that was the linchpin of their whole argument.
Woot was probably just one of the things they were threatening to close down and move out of state if Texas didn't give them a break. And I'm sure they had an argument ready as to why Woot wasn't a tax nexus for Amazon as a whole; there's a lot of really arcane rules that go into determining nexus.
The real losers at the end of all this are going to be the tax-free states, who ended up getting a lot of Amazon (and other mail-order retail) business because putting a warehouse there wouldn't risk triggering taxation. But if the tax loopholes are closed, there's not a lot of reason to set up shop there. They are going to be the losers in the end, I think.
Distribution center operated in Irving, TX from 2005 through 2011. Woot, in Carrollton, TX was acquired in 2010.