The temperature you change this way is only the electron temperature, which is primarily used to avoid having a step-function Fermi distribution, which makes convergence hard. So, this "temperature" is not physical, it's more a numerical "cheat", in a sense, although for some thermoelectrical calculations the electron temperature can be used to compute properties like the Seebeck coefficient.
What you need is instead to change the ion temperature, which is a bit harder. First of all, you need to consider "what is temperature" in this context, or more precisely what is the effect of temperature on \resistance. This is well known, of course - in short, the atoms vibrate, which means they no longer form a perfect crystalline lattice, which causes scattering, and that is where "resistance" basically comes from.
So the way to capture the influence of temperature in calculations like this is to perturb the atoms from the perfect lattice. This should be done in a systematic way, and fortunately QuantumATK has precisely such a method, called "Special Thermal Displacement" - see
https://docs.quantumatk.com/casestudies/std_transport for an example!
The main complication when using this method is that you need to evaluate the phonon spectrum of the system. If you have a simple metal and looking at grain boundaries, say, this is not such a big problem, as there are usually classical forcefields that can be used. But for more general situations (even a "simple" combination of two materials, like Ru and Ti as you have), one may need to resort to DFT for the phonons, which is a bit time-consuming (understatement). Or, find a way to combine individual potentials, or fit a new potential which is also possible with QuantumATK, but that's a whole other discussion.
Btw, since your initial structure was basically a combination of perfect crystals, what you actually already have computed is in fact the low-temperature case. It's the high-temperature situation that you obtain via the thermal displacements.
