Conceptually this reminds me of embedded messaging: every app provides its own inbox, instead of properly integrating with my email inbox. More walled gardens.
By offering sellers a built-in checking account, Stripe (and in turn Shopify) can decrease the time it takes to access money you've been paid. Same-day or next-day access, huge deal.
edit: I'll add, Stripe already offers immediate access to cash (Instant Transfers), but they charge 1.5% because technically they're extending credit. Stripe is eating their own lunch here. People won't need Instant Transfers as often and their profit margin on the interest sitting in the checking accounts will be much lower than the 1.5% fee they currently charge for Instant Transfer. But much bigger market.