I read your earlier post three times to be sure of a proper understanding of the family relationships. It's clear from your earlier post that Henry, Mathias and Simeon Baines are not in your direct line, and that you're interested in MRB who enlisted in the Choctaw County company described in some detail earlier. We agree that these are members of two different families who lived near one another and might have been related.
You said that MRB "is also listed in the same company as Richmond B Baines." Here we disagree. You must not be using the National Parks Service index or the actual service files recorded on microfilm, the standard resources used people who research Civil War records. Here's the NPS index --
These are based on actual wartime records. If your MRB had joined the 37th Mississippi Regt. after returning from prison, his name should appear on company rolls. These are complete through the summer of 1864, and do include records for RBB, who died on May 9, 1864. By the way, RBB is not on roll with the 4th Confederate (AKA 1st Alabama-Tennessee-Mississippi) as you suggested.
I would like to know what source you are using for the 37th Mississippi.
You have the advantage on me in having read pension applications for MRB. From the census we learn that he did not marry until 1865, and obviously he would have filed prior to 1920 rather than his second wife, Abbie. As a veteran MRB understood that his pension application would have been rejected if he had mentioned service with the 54th Alabama Regiment, as he should have. Since the pension board would have had the same problem verifying his service with the 37th Mississippi, MRB must have supplied signatures of two witnesses to support his claim. A further look at the pension should support my assertion. If you don't mind, I would like to know who these men were.
A check of the 1860 census reveals only one man named Barnes living in that county, his name being Andrew J. Barnes. This man served in Co. "D", 40th Alabama Regt.
As explained earlier, Company "F" of the regiment you are calling the "1st Alabama" later became Company "F" of the 54th Alabama Regt. MRB joined in 1861, just as the MRB who signed the oath of allegiance stated. If there's an easy explanation for a soldier named Mathew R. Barnes serving in the very same company that Mathew R. Baines joined in 1861, I cannot imagine what it may be.
The name "Baines" can become "Barnes" simply by mistaking the 'i' in Baines for an 'r'. This is an easy mistake to make, especially when reading handwritten notes in cursive. I'm convinced that Mathew R. Barnes of Choctaw County, 54th Alabama Regiment, is one and the same as your MRB. His oath of allegiance, by the way, lists "no family", which matches the 1900 census, which gives a date of marriage of 1865.
I'm sorry to be offering conflicting information. It's clearly unwelcome, and I can understand why. Other researchers may be interested in the facts discovered during this research effort. Evidently you have determined to disregard my research, but they may benefit from it.