What are they purchasing within your own portal? It sounds like instead you could implement the usage charges with the Billing API. This way you won’t need to charge them when they install the app, only when they purchase whatever is in your portal.
Shopify is pretty strict about their Billing API requirements. If there are any charges accrued while using your app then it needs to be handled by the Billing API. If your app falls under a special circumstance however, you can request a Billing API exemption.