The C46 came along later, and had reliability problems at the start. I checked, and the first C46 didn't reach the AAF until May, 1942, meanwhile, almost 1,000 C47s were built in 1941, and over 5,000 in 1942. C47 didn't take as much maintenance or use as much fuel, and was a good performer. So the Commando became a supplement to the C47 fleet.
My Dad flew for the first time when he was taken from Fort Dix to Nevada for a nuclear test in the 50s. They went in C46s. They were much delayed as two of the aircraft assigned to them crashed, while two two others missed the mission with mechanical problems. Dad always said flying in them bothered him more than the bomb.