Yea it's a bit annoying, tried booking HKG to CTS and it doesn't show any of the domestic legs so naturally I cannot connect in Tokyo. So the online booking system tries to route me through other cities in Asia with direct flights to CTS.

I am going to book HKG - CTS through the other cities and call in and hope they don't charge me a fee to book through the phone, since you can change the routing free prior to 21 days