I understand what you are asking. And, in an ideal theoretical system, what you are saying would prevail. But, the real world doesn't work like that, and the equations for an elasitic medium with mass/inertia is only an idealization. In the real world there are also dissipative forces at work, and, even though, in many situations, these force are small, they have a cumulative effect and allow the systems we are discussing to relatively rapidly reach static equilibrium.
When I said the response of the rod is instantaneous, what I really meant was that the response is virtually instantaneous. This is because the stress disturbance travels at the speed of sound (predicted by the dynamic equations you derived, with inertia included). So for a rod only a foot or two long, the response is virtually instantaneous.
You were talking about the transient temperature effect and comparing it to the transient stress effect. First of all, the transient heat transfer equations are parabolic, rather than hyperbolic. So the disturbance front is diffuse rather than sharp. Secondly, the speed at which the diffusive front progresses is much slower than the speed of sound, because the thermal diffusivity of the material is low. So, if you put a turkey in the oven, it takes hours for the thermal wave to reach the center of the turkey.
Here are two examples to help understand what I'm saying.
Consider a mass suspended on a spring, and you pull the mass downward, and then release it. Theoretically, the mass will oscillate up and down forever at the exact same amplitude, and the stresses and strains in the spring will continue varying forever. But, in the real world, we know that the amplitude of the oscillation will fairly rapidly decrease in time, and the mass will soon come to a new static equilibrium position. This is because of air drag acting on the mass which dissipates the kinetic energy.
Next, consider the kitchen chair I am sitting on right now. This chair is wooden, and has wooden legs. The legs of the chair are in compression, but there are no dynamic oscillations occurring in the legs of the chair. The stresses and strains in the chair legs are constant. This is due to the damping provided to the chair by the kitchen floor on one end, and my fat butt on the other end. This damping caused the oscillations to die out. So the chair and its legs are in static equilibrium. How long did it take to reach static equilibrium? The response to my sitting down was virtually instantaneous.