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Hello Adavies,
Did you ever get your answer? I am in a very similar situation and wondering what the result of this was. I didn't see any responses to your questions.
The way I am setup currently is; my app is a free app that the merchant utilizes for 3rd Party services. The merchant is paying me and I am paying the 3rd Party. With this setup, it is not clear whether I should be utilizing the Shopify Billing API or if it is ok to use my integrated 3rd party payment gateway.
Thank you!