Repetier
It does not really matter if you use M104/M140 or SET_HEATER_TEMPERATURE when klipper works as supposed. SET_HEATER_TEMPERATURE is needed if you have multiple beds or chambers which is why it is included now and preferred if name is known.
Haven't tested it on klipper printer for now and due to time it has to wait a bit. But I wonder that no one else is having the problem as well. Especially since these functions are identical to all firmwares.
With that start gcod ein klipper server even would not need to set temperatures jsut calling PRINT_START and it should be set even if we would not do it.
There is one reason why server would stop sending M104/M140 and that is firmware says it is unsupported. Then it would strip all these commands from being send later until it is reconnected. In case of klipper this happens if we receive:
// Unknown command:"M104..."
You could try instead deactivate printer and activate in server. That flushes the list if it existed but does not restart klipper. If it persists it is more klipper if it is gone it might come from unknown command.