I doubt Amel changed the size of the cavity. I ordered the batteries with a fellow 54 owner with a much earlier hull number and he had he same problem. I do know the problem was in the few centimeters region but that is all it takes to prevent you from installing 13 (12+1) batteries in the cavity.
Keep in mind that the cavity is much bigger then the hole you have to put the batteries trough. I’m not sure anymore but that may have been the problem in the end. It was like playing Tetris with very heavy batteries.