While I agree that there are many confusing jurisdictional pitfalls in incorporation and banking, this isn't one of them. SVB in particular has customers all over the nation and it is ludicrous to suggest that a state's tax authorities would go after customers of banks based in their state as if they had jurisdiction over those customers' business conducted outside the state.

Law is a messy business, but they have literally taken the most typical arrangement for startups in US accelerator programs as the first template for Stripe Atlas. I can't imagine a safer set of choices.