The men would have been paroled before leaving Ship Island. While this could have been a limited parole - a promise not to attempt to escape en route to Vicksburg in exchange for fewer guards and less restrictions while in transit - the standard practice would have been to parole them for exchange at the starting point. These were legal proceedings, each step had a legal meaning.
The men who were released on parole at Camp Townsend but who did not receive a final parole at Meridian under the surrender agreements were men who were not present for duty at the end. Some may have gone straight home without leave. Some were likely sick, sent to Confederate hospitals, and furloughed home as "paroled prisoners of war." I have found many records of men furloughed home from Richmond as "paroled prisoners of war" having to stop at Wayside Hospitals in Mississippi for further medical assistence. Until their name appeared on an official exchange list, their status was "paroled prison of war."
The official exchange declaration had to be made at Richmond (I have not yet found that Colonel Robert Ould delegated this responsibility) and the state of affairs in Richmond in March 1865 was approaching chaos. Perhaps these men released on parole at Camp Townsend were never declared exchanged. Have to keep looking for that!
Those who rejoined the army needed to be accounted for under the surrender agreement. This resulted in the additional "final paroles" dated after 4 MAY 1865 at Meridan. Those who were not accounted for by this process were expected to report into local provost marshal offices to be accounted for and given their final parole. Those who could show they were already covered by their prison release parole did not have to give a second parole.
Many overly enthusiastic Federal provost marshals did it anyway. Looked good on the books!
Going home early without a parole kept many a needy veteran from getting a Confederate pension at the end of their lives.
Camp Townsend apparently had a limited life. There is a piece of correspondence in the OR Series II dated 6 MAY 1865 (two days after the Citronelle surrender) in which Confederate Lieutenant Colonel H. A. M. Henderson is urged to come and get 2,500 Confederate prisoners of war off of two ships at the Vicksburg dock. Henderson was addressed as an officer of the Confederate States Army, and the only Confederate territory still in business was the Trans-Mississippi. All of the Confederate government operations east of the Mississippi River ceased to exist as legal entities with the Citronelle surrender on 4 MAY 1865. Presumeably then, Colonel Henderson was to take these men aboard a Confederate supplied transport and move them to the Trans-Mississippi. Otherwise, the Federal authorities could have released them at Vicksburg to return to their homes east of the Mississippi.