Hi @amiewilt
What you are describing is a known use case. Having customers auto-logged in when they re-direct from the API to Web Checkout is a security issue. Since the checkout URL is unauthenticated, then you’d have a checkout URL that could be shared or stored that gives direct access to a customer’s details. So when a customer is associated with a checkout, we require them to re-login to validate that they have access. You can read more about the issue here.
If you are using the Mobile SDKs, this can be resolved by passing the customer access token through the custom header of “X-Shopify-Customer-Access-Token” in your request to load the web checkout URL. See here for more details.
On web, the only way to accomplish this right now would be to use Multipass and its API to associate the customer accounts instead of using the mutation “customerCheckoutAssociatev2”. This will allow customers to be logged in and be directed to checkouts while remaining logged in. However this functionality is only available for Shopify Plus merchants right now.