The comments about the lack of weapons situation that was in the report mentioned was made after the means of transporting such weapons across the Mississippi river and the Trans-Mississippi department had been isolated from the rest of the Confederacy.
This is still not to say that the arming of the Blacks soldier in the southern army was not going to be a problem. It would have been. But we would also be looking at a reverse situation where as the Blacks had been used in the past to free white soldier to the front lines, the blacks would now be used to fill the ranks of those who had ceased to be able to serve and to fill the thinning ranks with the muskets that you did not have men to carry. In 1864 had Lee been able to simply replace a portion of his casualities in his ranks alone by having a black soldier to pick up the fallen musket of his white soldiers Grant would have a far harder time than he already did to get to Richmond. And bare in mind that the ANV did not lose control of any of the great Battlefields during Grants march to Richmond. Grant abandoned all battlefield pickup ordances to the Confederates.