Currently, if a Payment Gateway does not store a payment method, you cannot manage the specific gateway in the Payment Methods page. This is for example the case with PayPal: you can pay an invoice using PayPal, but not set or add PayPal as your default payment method in the Payment Methods page.
I'd suggest adding the option to set/add any gateway that a WHMCS user supports as a default option. If the specific gateway doesn't allow you to automatically bill the specific gateway recurrently I'd propose that a status indicator tells you so, and that a separate reminder mails gets sent to the client when an invoice is due for payment reminding that a payment gateway is selected that doesn't support automatic billing.
For my end I'd appreciate a feature such as this for PayPal and iDeal via Mollie.