We're all futurists here except when that means losing affiliate revenue and/or no longer having a tax dodge. It's just a matter of time before there's uniformity between the online and brick and mortar worlds, and Amazon is simply seeking delay. Per Sinclair "It is difficult to get a man to understand something, when his salary depends upon his not understanding it!"
Option (2) is really, really bad, especially for small businesses and startups. You don't want to all of a sudden have a successful brick and mortar spice business in New Hampshire and find out, holy cow, you're in arrears for lack of tax payments in California! That'd be a business-killer.
The process matters.
And no, Lab126/A9/their other affiliates don't count, as they are not the company selling you the product.
The affiliate program might be the strongest legal argument for in-state presence, but it's far from the only one. Apart from the subsidiaries, there's also the more than $3 billion they get from CA residents.
I think everyone here should have to disclose competing interests on this topic:
full disclosure: I work for a company (part time) that makes most of its money from Amazon affiliate revenue (but I personally am not taking Amazon's threats very seriously).