I remember reading a dev post that it isn't the court physician directly converting people, it all happens through preexisting mechanics like the heritage focus (Which I believe looks for high learning when selecting guardians) or friendship, and all Reaper's Due has done is increase the number of different religions at the average court.
Come to think of it, You'd see this kind of thing pretty often in older patches when you extinctify a religion, too. Like if you take over the entire muslim world you'll sometimes notice all the muslim courtiers flee to Scotland or someplace like that, because they've got nowhere else to go, and inevitably one of them will convert someone landed. I see it most often with Armenians in early state dates.