Temperature is a measure of the average energy of the molecules in some material. Clausius needed to define temperature as a thermodynamic quantity; thus it was not necessarily the value we measure with a thermometer. The temperature is the change in energy divided by the change in entropy (T = ∂E/dS). This was to make sure the temperature was a thermodynamic quantity and not just a physical manifestation of that quantity.
If energy is easily converted into other forms of energy then the normal thermodynamic concepts are true. This provides the route to equilibrium and the measure of efficiency of energy conversion through the action of entropy. But if the energy of a system is not heat energy and is not readily converted to heat energy that energy system is isolated and the energy equations are only applicable within. Then the definition of the thermodynamic temperature will be internal to that system. Such a temperature then can affect the outcome of entropy relationships within that system.