Here’s the image of the Little Boy being loaded into the Enola Gay’s bomb bay for reference.
Basically, the main difference between the “Silverplate” version of the B-29 compared to the base version is that it removed almost all the defensive armaments to save weight for the long range mission they were meant to take, while the bomb release mechanisms were only modified a bit; they kept the original bomb bays of the base B-29 variants, including the unoccupied one as seen in this image.
So, in theory, it would require only changes in bomb release mechanism for the base B-29 variant to carry a Fat Man-type bomb or similar weapon, which is already demonstrated that it is possible via the Mark 6 atomic bomb we have in-game.
