The only significant empty PCB space I'm seeing is directly under the SSD slot, about a square inch that may have been necessary to keep empty to provide clearance for components hanging down from the SSD module. Most of the rest of the board appears occupied by heatsink or various shield cans with a black covering.
probably heat issues prevented them from doing that.
I'm surprised it doesn't overheat already. My 4TB on an M.2 2280 form factor runs at 60+ C. Compressing that down would make it much harder to dissipate the heat.
60˚C isn't a temperature worth worrying about. And if that's what your SSD is at when idle, then it's entirely due to having a bad SSD controller—the part that is absent from Apple's storage modules.