Well, I think the main difference between the .41 and the .44 was that the .44 was developed to be a hunting round. The .41 was developed to be the next big police caliber. It never caught on because of the recoil.
The .44 when hand loaded has more case capacity and can use slightly heavier bullets, the .41 has a better ballistic coefficient and more versatility in medium framed guns.
I believe that they can cross over into each other's territory and do both things well, but one has more potential as a hunting round and one has more potential as a self defense round.