First, the Commando wasn't unique in having a 'stepless' cockpit design- the Boeing 307 Stratoliner, for example had them. Other military aircraft too had them, due to a few reasons like pressurization and the excellent visibility (He 111, Ju 388, B-29 Superfortress, the list goes on... etc) they offered.
While it's true that having this design improves the aerodynamics of the aircraft, there are other things to consider.
- More complex a shape, more difficult is it to manufacture usually (which increases cost). Aircraft design, then as is now is a trade-off. The designer has to select a nose design based on trade-offs between various factors like aerodynamics, ease of manufacture, location of LRUs etc.
In fact, during original design of Lockheed constellation, multiple nose configurations were considered, which included completely faired nose (along with 'bug-eye' types). That the conventional arrangement was finally selected indicates that the designers decided that the drag reduction offered wasn't worthwhile.
In order to achieve ideal visibility characteristics for the pilot, the entire nose and cockpit of the CW-20E was redesigned to incorporate a flat glass windshield with negligible refractive and reflective errors. At the same time, the field of vision was increased.
indicates that this was definitely a consideration.
The present scenario is different- better materials and manufacturing techniques are available- not only for the windshields reducing errors and quality issues but also the fuselage shell, enabling optimizing structures for better aerodynamics.
I believe the Commando erred on the side of the aerodynamics- it had fairings between the top and bottom fuselage halves, which were later deleted, as flight tests showed they provided no improvement in performance. According to George A Page, Chief Engineer St Louis Airplane Division of Curtiss-Wright Corporation, the C-46 had not only stepless cockpit, but also 'tunnel type' cowlings to reduce drag.