Billing API Multi Store Solution

Shopify Partner
7 0 1

I have a question regarding the billing API. I've checked the forums but unfortunately there isn't any helpful information for my problem. If you could take a quick look at my issue that would be much appreciated.
My questions below:

Does anyone have any experiencing with the Shopify Billing API? I've looked into the forum, however, the solution provided would not make sense if the customer has multiple store integrations otherwise they would get billed multiple times for the same subscription fee from our app.

Any advice would be much appreciated!

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