Thanks very much for your suggestion to improve the Stripe integration by allowing multiple cards to be stored against a booking.
At the moment, we are limited to storing one card only as when you choose to charge a stored card, the request is sent to Stripe to retrieve the customer and unique booking reference.
As only one customer can be connected to a booking reference we'd have to re-visit the integration to make your request possible.
You can however apply multiple charges to different cards, but I appreciate that this would require the chargeable amount to be known in advance.
If there is any further development in this area I will update you via this request.