We[1] use Stripe[2], Braintree[3], Coinbase Commerce[4], and GitHub Marketplace[5].
We built our own quote logic including prorating, etc. then apply that as recurring subscription using Braintree if customer wants to pay with PayPal, or Stripe if customer wants to pay with credit/debit card.
Is there any use policy restriction on Stripe, Molly and/or Braintree that would prevent one to dynamically select one or another payment provider depending on the quoted fee for a given customer (card type, country, currency...)?
Not sure, but I know other companies use multiple payment providers too usually for redundancy. We would use Stripe for everything, except Stripe doesn't have the ability to accept BTC or PayPal.