How can I customize the Shop Pay checkout process on Shopify?

We are implementing some customization of checkout.liquid, but when folks choose to use Shop Pay they are redirected to the Shop Pay checkout that appears to be a clone of the original Shopify checkout, without using the customized checkout.liquid file. Is there a way to customize that? Or have Shop Pay work like other payment processors and redirect back to the standard Shopify checkout flow?

@bbarr Did you ever find a way to customize this Shop Pay checkout experience? We’re dealing with a similar issue in our store and haven’t found a resolution.