Yes, there is a difference.
When you set the temperature in the electrodes, before the calculation, this influences the self-consistent calculation and changes the electron distribution in the central region indirectly, since there are now different boundary conditions at the interfaces to the electrodes (because of the excited electron distribution in the leads).
If you only change it in the analysis of the transmission, then you use the same electron distribution for the central region, but change the distribution in the leads for each calculation of the transmission spectrum.