Zhao Fu planned to leave the rest of the Body Rocks to be used in the future on the four boundaries of Great Qin. Those places were the boundaries between China and other nations, and because they would definitely suffer many battles, they needed to have powerful defenses.
As the central city of Great Qin, the Great Qin City was incredibly important. However, if the enemies were able to reach the Great Qin City directly and attack it, that meant that Great Qin would most likely lose.
After all, if a faction's core was attacked, even if it wasn't destroyed, it would be crippled. As such, it wasn't enough that the central city was powerful; the other cities also needed to be powerful to create defensive lines.