My employer is exploring the possibility of developing our own custom app solely for our own usage to support our subscription business. I saw that there are requirements for subscription apps listed in section 14 of specific-requirements-for-certain-app-configurations. Do these requirements only apply to public apps or do they also apply to custom apps?
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Those requirements are only for public apps that want to be listed on the Shopify App store. If you want to make a custom app using the subscriptions API, you would still have to request it via the partner dashboard: https://shopify.dev/apps/subscriptions#requirements
What about if we want to make a custom app for subscriptions for our own usage that doesn't use the subscription API? We're concerned that the current implementation of the subscription api doesn't support our subscription business as it currently is. Our partner for the development of the app would likely be an internal employee of the company.