No first hand experience with Thai Smile, but in general check-in agents (TG) are very good at and experienced in checking bags to final destination when on a separate TG ticket HKT-BKK. Check-in agents do that all the time. The reason is also that then pax will clear immigration at HKT and be able to proceed to international departures level with a C.I.Q sticker upon enterring the terminal from the HKT flight.