In-App preorders with third party payment provider/Stripe SDK - what API is compatible?

Shopify Partner
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Currently, our App is under review, and during the review  process apparently Shopify is forcing our in-app payments through their payment gateway and not our external stripe SDK payment provider. However, when we test it on our shopify stores it appears to work, and we have also tested it in incognito mode as well and it works. All of the other features appear to work as well and pass with flying colors.


So, with regard to our app-feature with a separate check out, how can it process these payments with an external payment provider (Stripe SDK)? What API makes it compatible with Shopify?


In context, specifically the issue appears to be with our  'pre-order feature,' -- we have a subscription based payment feature (through Stripe SDK) which allows the merchant's customers to subscribe to the crowdfunding campaigns where they are not charged initially on their subscription and only charged on the payment due date which is upon the campaign end-date and then the discount is applied.


here's a screencast:

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