Perhaps the webmaster for that website would direct you to contact information from the author. You have some good questions and I would be interested in reading the response. I have read the OR's and the Union versions do not match up well with the Confederate reports or each other.
One thing I believe I know about war is that when the attacking force offers surrender terms, but ultimately must storm a fortified position, there is a deep resentment (sorry I cannot think of a better word) on the part of the attackers. There was a general melee in that engagement, there were Southern (black) defenders who were considered traitors, immense provocation by the pillaging of Union forces upon local civilians and poor leadership for the Federals.
One might argue the Confederate leaders had motive to cover up facts, but they did not even offer to do so. Forrest, knowing about the huge push for propaganda in the North, decided to let President Davis deal with the matter once he got the report, weeks later. And time was an important factor. On the other hand, the Union command under Major Bradford wasted no time is covering his assets and his version was gobbled up by the Lincoln approved Northern press.
Here is an excerpt from "Nathan Bedford Forrest, First with the Most".
"Major Bradford signaled to me that we were whipped," Captain Marshall, commanding the gunboat New Era, told the Congressional committee. "We had agreed on a signal that if he had to leave the fort, they would drop down under the bank, and I was to give the rebels canister.
And so, with the flag of the fort still flying and with arms still in their hands, the garrison dropped below the bluff, with apparent intent to continue resistance there, while the gunboat was "to give the rebels canister." But not a shot was fired from the gunboat. Instead, the prudent Captain Marshall, having found that be was nearly out of ammunition and fearing that the victorious rebels would turn the guns of the fort on him-as they actually did-closed his portholes and steamed away out of range.
When the fleeing garrison found that there was to be no blast of canister at their pursuers, panic seized them. Some continued their resistance; others thought only of safety in flight. As they rushed southward along the riverbank, they were met with a volley from the detachment under Anderson, which had come down to the steamboat landing to prevent reinforcements from coming ashore from the approaching transports, and which now fired their first shots in the assault. Turning the other way, the demoralized troops of the garrison met the fire of Barteau's men, beneath the bank on the other side of the fort. Others rushed into the river where they were shot or drowned-and all the while the flag of the fort still flew from its staff, until Private Doak Carr of the Second Tennessee (Confederate) cut it down.
"For the survivors it was a fortunate occurrence that some of our men cut the halyards and pulled down their flag, floating from a high mast in the center of the fort," reports Anderson, who was under the bluff. "Until this was done our forces under the bluff had no means of knowing or reason for believing that the fort was in our possession, as they could from their position see the flag but could not see the fort."
What happened under the bluffs was described by Lieutenant Learning as a "horrid work of butchery," which continued from the fall of the fort "until dark and at intervals throughout the night. Others who testified, including both those who were there and those who were not, were more profuse and harrowing in their detailed accounts of rebel savagery in the 128 pages of the report of the Congressional committee. And there can be no doubt, nor has it ever been denied, that some men -perhaps a considerable number-were shot after they, as individuals, were seeking to surrender. However, as Second Lieutenant Daniel Van Hom of the colored artillery regiment put it in his report, "there never was a surrender of the fort." Instead, as Colonel Barteau described the situation in an interview published in 1884, "they made a wild, crazy, scattering fight. They acted like a crowd of drunken men. They would at one moment yield and throw down their guns, and then would rush again to arms, seize their guns and renew the fire. If one squad was left as prisoners ... it was soon discovered that they could not be trusted as having surrendered, for taking the first opportunity they would break loose again and engage in the contest. Some of our men were killed by negroes who had once surrendered.
There are some scholars on this board that could contribute a lot more, but probably not unless this is moved to a separate thread.