Get the point that the S85 engine was originally designed for the SMG II and using the MT in the E60 was in fact not a priority. However, in designing the E9x M3, given it was offered first with a manual (and was the intro to the market and the base car for all major tests) in addition to modest gearing changes (and a higher diff ratio), don't think there's much evidence to say that the S65 was not developed with the MT as the core transmission. Isn't the torque curve for the S65 engine more "MT friendly" vs the S85 to begin with?
When I ordered my car, I was going to go with the DCT, as I knew on paper it would be the fastest iteration of the M3. I was 90% there decision wise, but wanted to make absolutely sure, so I test drove the only MT available at the dealership at the time which was a convertible. Yes it felt slower (tranny plus extra weight), but it was soooooo much more fun to drive....at that point I thought that the MT was the transmission meant for this car and changed my order with the CA immediately after the drive.