it's not just a basic geometry problem, it's an engineering problem. You need to account for far more details.

It's more complicated. You can't pack the battery at 100% anyway, because you need cooling. Cylindrical cells are also more rigid, so they need less supporting material, or they can even be a part of the support structure itself.

With cylindrical cells, you have more leeway in the overall shape of the battery pack and can fill nooks and crannies with them.