Hi Lana. The person who researched your ggggrandmother does not appear to have given you enough information to check their research. Did they mean to say that Milly's name was Milly Stewart, or do we only know that Milly was her first name?
Was the vital statistics record a death certificate? What was her name at death, what year did she die and what was her age at death?
There's no evidence (that I recall) that Thomas Stewart had a slave named Milly when he died. If a person's name was Milly Stewart, it is more likely she was a member of the Stewart family.
If a person's name was Mason, and they were free before the Civil War, you would need to do more research to see just when they became free since the person might descend from the Mason family that was free from colonial times.
Paul