My great grandfather, who owned a small railroad and lumber business in central Georgia after the Civil War, was referred to frequently as "Captain." I learned that that was not a military rank, but an honorific for persons who employed prison labor. (Think of the lyrics to "I've Been Working On the Railroad" -- "Can't you hear the captain calling ...."). Was that honorific applied nation-wide or regionally? When and how did it start?
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The word captain was never specifically “an honorific for persons who employed prison labor”. It is a more general term. It has always been used to mean the chief, or head, of many types of gangs of men. Your example is typical.
Consequently, the origin of your great-grandfather’s honorific is the same as the origin of the word captain itself, which is ultimately the Latin word caput, from PIE *kaput- (head), so literally head-man.¹
NED attests this usage at sea:
in various trades:
in schools or forms (grades) of schools: