Amazon is going to demand tax concessions. I can't see Houston granting them.
Houston does tax deals, though more importantly an HQ as large as their existing one will likely be outside of the City of Houston and still be within what most people refer to as "Houston" (like ExxonMobil's Houston Campus). Houston has the talent, the demeanor, and the amenities for a major HQ, but I think it will be quite easily outdone by other applicants.
If Amazon came to Texas, I would expect them to go to San Antonio. The vibe in San Antonio is excellent, it draws workers easily, it is relatively LCOL, wages are also lower, it's less prone to any sort of natural disaster, has a great green/environmental scene, and it's well situated within the Texas Triangle with easy access to Austin for their nightlife and the outdoor offerings of the Texas Hill Country.
If they're supposed to be twin HQs one in the same time zone is preferable (so CA would be a big likelihood). However if the point is to make certain operations easier on top of expanding, I would expect them to move to the eastern time zone so they can have better coordination with Europe.
8AM in Seattle is 5PM in Berlin (4PM in London), and 5PM in Seattle is 1AM in Berlin (midnight in London). 8AM in the Eastern Time zone is 2PM in Berlin (1PM in London), so you have three or four hours of solid overlap. If you've ever worked with major European companies you know you're SOL if you need them at 5:03PM, it's just a cultural thing you have to deal with.
Amazon has invested heavily in their European operation, so I wouldn't be surprised if that is driving part of the 2HQ idea.