Kiso shop and Tokyo shop, both in Japan, as mentioned above, about 150miles apart. Most of the Signature Series custom shop stuff and Original Series stuff tends to be Kiso Shop built from what i've seen, many high end custom orders and artist order guitars are from the Tokyo Shop. Kiso Shop does still handle a load of individual custom orders though.
There is also the Craft House (CH serial, domestic japanese orders) Sado Shop (SO serial, this is mostly for bolt on guitars!) and Technical House (TH serial, domestic japanese orders, insane shizz)
Key point is that rather than compromise on the hand built ethic, and have giant facilities with CNC machines and medicore staff, ESP have multiple work shops and custom shop facilities around Japan, enabling them to spread the high volume of orders across multiple shops, without having to compromise their traditional 'luthier built' custom instruments.
IE, hire/train more luthiers, built more workshops. Rather than compromise and modernize to machinery and automated processes.