Not only is the "Southern Girl" melody the same as "Bonnie Blue Flag" but the author obviously meant to refer to it--striking similarities in lyrics:   e.g.   

"Hurrah, hurrah, for Southern rights, hurrah"

becomes

"Hurrah, hurrah, for the sunny South, I say"


The Irish connection is also close:    "Bonnie Blue Flag" was written by an Ulster immigrant, Harry McCarthy.

As is well known, the Irish were very well represented on both sides of the conflict--to say the least. Partly of course since they were often "substitutes" for a "$300 man" in the North.