I am thinking of the thermocouple as just two wires twisted together and the twisted section being heated (hot junction). If one of the wires has a larger amount of the wire heated, but the same temperature difference, the voltage reading is the same for a smaller area.
From my understanding of a thermocouple, the voltage is generated from the Seebeck effect where the charge carries with more energy from the temperature increase will migrate to the cooler end. Surely then, if more of the wire is heated, the electrons will have a higher kinetic energy and therefore there would be an increased voltage? I can't see why this isn't the case however.