There may be some clue in his full military service records at the National Archives on why he transferred to the 21st Mississippi. He likely had a relative in the latter unit.
This excerpt from your post, especially the last sentence, leads me to believe John W. Hunter transferred to the 21st. Mississippi to serve with his neighbors and possible relatives.
From the NPS's CW Soldier's database, he is listed as a member of Company E, 21st. Miss.
Company E, the Hurricane Rifles, was raised in Wilkinson County according to the capsule history of the 21st. Miss.
From census records of Wilkinson County, MS (1830-1860), I find John/J.W. Hunter, born abt. 1838 (MS), in the household of Willis & Rebecca Hunter.