Just booked PNI-TKK UA 154 island hopper through the YYZ office. the IST call centre had problem locating TKK airport (which is not included in the list of airports on TK.com).
Sales office uses a different DOS-like generic booking system and had no problem entering "TKK".
I did have to tell the agent at YYZ office that it's a domestic flight costing only 7500 miles, instead of 15000 miles for regular in-region flights. She had to change some entry to get the correct mileage. 0 tax on this route.
Overall, it seems the system is now working. Finally!