The setting in question which I currently need to manually change is in file /wp-content/plugins/woocommerce-gateway-paypal-powered-by-braintree/includes/api/requests/abstract-wc-braintree-api-vault-request.php
The setting:
‘failOnDuplicatePaymentMethod’ => true,
This needs to be set to false if you want to allow duplicate cards in the vault.