Yes, you can absolutely save the card on file and then create the subscription all in one checkout experience for the customer. Once the customer submits their card information in the Web Payments SDK your server will take the generated token from the Web Payments SDK and call CreateCard. Once it has the card_id from that call your server can then call CreateSubscription.
As for merged customer profiles the card on file will still be stored on the customer profile. Merging won’t disable the card. 