You asked about James Boykin and the surrender at Citronelle. The surrender agreement was made there, but Boykin received his parole at Mobile on June 13, 1865, several weeks later. Only General Taylor, one staff officer and two servants were present at Citronelle.
A parole is not evidence that a man was then enrolled in Confederate service. A parole signed by a Federal military officer offered protection from arrest for the bearer's activies against the United States, whenever they happened.
Evidence of his Confederate service would include pay records, orders, requisitions and other papers signed or issued to an officer. After Boykin resigned his commission in February 1862 we have no papers showing that he ever received a new commission. He is one of a large number of men who did their best to secure a Confederate military commission but failed to do so.
To the best of my knowledge when the war ended he was enlisted as a private in the Alabama Senior Reserves, probably absent on detail.