A thermocouple produces a voltage only in reference to the other junctions in the circuit, if they are at a different temperature. The Omega tables are referenced to 0 degrees C, but could be referenced to any other temperature. It is just that 0 C is easy to get. When a complete circuit is made, current flows and energy is transferred. The hot junction losses heat, the cold junction gains heat. The instrument simply references to 25 C, so when the input is shorted, it believes the thermocouple is at that temperature.
I hope this isn't so poorly written as to confuse the issue.
When I used to work at the local college, we had a thermocouple demonstrator w/ a circuit made of 2 different materials, w/ about a 1/4 inch cross section. When one junction was heated more than the other, it could produce currents over 100 A.