Can we customize checkout and payment for multiple payments using an app?

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Hi, we are working with a client who is building a business that enables people to try things on at home.  The plan is to build an embedded app to help merchants manage the process.  The process requires us to customize the checkout and payment flow.  We need to charge an initial payment in the checkout flow but then the process requires an additional payment(s) or refunds after the customer decides which products to keep or return.  The business model is also commission based on each transaction.  Is something like this possible using the Shopfiy API and apps model?  Thanks in advance for your insights!

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