Usually yes. There is even a little PCB between the mainboard and the chip to get enough area for the thousands of pins. But this is not the case if they stack

Usually yes. There is even a little PCB between the mainboard and the chip to get enough area for the thousands of pins. But this is not the case if they stack the flash chips with the controller chips. Then only a few external pins are needed for communication and power. But the flash chips actually need the silicon area for all those tiny flash cells.