Yes, the Epic store enables this exact scenario. Lots of free games on Epic make all of their month through micro transactions billed entirely through their own systems. See Rocket League for one example, but there are many.
UPD: At least while ago in 2019 Epic claimed to give a choice of payment processor to use for games on their store: https://www.gamesindustry.biz/articles/2019-12-06-epic-games...