It really depends. In the case of the C-46s, they were delivered to the Army and surplussed when the war was over. Civilian operators came up with their own paint schemes and flew them that way. When they get restored back to a military configuration, they get painted again, and sometimes things are removed or put back that were changed by civilian operators.
China Doll has a distinct Malathion hint on hot days as for a while it was used as a pesticide sprayer. I don't have the full history on Tinker Belle, but China Doll was delivered late in WWII and did not see service during the war. She was used as a regular Army transport post war and there are some oddities in it if you looks closely. For example, on the fuse panel, there is a fuse labelled "Missile power". The early missiles had to have power applied all the time for their gyros and guidance systems, so there was a fuse for that power when they transported those missiles.
If memory serves correctly, China Doll was surplussed in the 1950s and picked up by a handful of civilian operators for cargo and pesticide spraying before being picked up by the DEA for running illegal narcotics. I believe that China Doll was picked up by the CAF SoCal wing in about 1983 and had a horrendous paint scheme with a "Humpty Dumpty" type nose art. The egg was wearing a coolie hat and had a caricature of a chinese face. It was called "ole 94". Incidentally, the new paint scheme nose art "China Doll" was painted by Tony Starcer. Tony Starcer was responsible for many nose art paintings during the war (hundreds!), including "Memphis Belle".
When China Doll was repainted again a few years back, they were going to lose the China Doll artwork. Fortunately, Pat Seca, the wife of one of the CAF members down there did an exact replica of the artwork to preserve Tony's work. What's even more interesting about that is that Pat is not an artist and had only done some pencil sketching before that! Here is a shot of Pat's wonderful job.