To clear the matter of pension eligibility, a veteran had to apply in his state of residence. Since Austin lived in Savannah, he had to apply in Georgia no matter where he enlisted. He could not have applied in South Carolina without first leaving Georgia and establishing residence. That's the advice he's getting in the letter.

I'm troubled not to be able to identify this man on the census prior to 1900. In that year he's a resident of Savannah, an architect, claims to have been born May 1852. In 1910 he is simply a carpenter, does odd jobs, and born ca. 1852. Note that another man named Franklin B. Austin lived in South Carolina. He was almost ten years older, and could easily have been a Confederate veteran.

I don't see your ancestor on the 1880 census for North Carolina. I'm not certain that he's to be found anywhere else. Have you been able to locate him in that year or earlier?