How to charge merchants without using the Billing API

For Shopify Partners developing custom apps for clients, the documentation states that apps using the custom distribution method are unable to use the Billing API to charge customers. How then are customers charged w/o the Billing API?

https://shopify.dev/docs/apps/distribution#capabilities-and-requirements

Hi Terrencecooke,

If your app is not going to be on the Shopify App Store, then you would have to set up your own method for charging clients who use your apps.

Okay, so custom apps must handle client billing separately.

Lastly, if I create a public app but want to restrict access to a specific client or a small set of clients, can this be accomplished somehow by making the public app unlisted?