The C, P and T symmetries came from the equations due to Schrodinger, Klein-Gordon and Dirac. These partial differential equations depend on time and position. By changing the sign of time and position, these equations remained unchanged, so here is the origin of P and T. The C symmetry resulted originally from Dirac's equation. Since these equations are very good at describing the behaviors of particles, we can safely say that C, P and T came from observations.
After the discovery of the weak interaction, C and P turned out to be violated, and the hope was that their combination CP is still preserved. After the discovery of the violation of CP, the hope moved to CPT. So, the experimental data said that each of C, P, T is respected when no weak interaction takes place, otherwise we should be happy with the combined CPT.
So, I think that the answer is that the experimental data told us that the universe is T-invariant, then when the weak interaction was involved, it told us that CP is violated, and from CPT that T is violated. And CPT is not specific to the standard model, it results from the Lorentz invariance and the fact that the energy is bounded for below.
A presumable CPT violation would imply the violation of the Lorentz invariance (http://en.wikipedia.org/wiki/CPT_symmetry#CPT_violation). So, if an alternative theory wants to distinguish itself by experiment, it should predict violations of the Lorentz symmetry. The theory itself will say the regimes in which this violation occurs (I bet that it will be at the Plank scale!). In this case, probably the Lorentz violation will imply with ease the CPT violation.
I find it very unlikely a violation of the Lorentz invariance, because this principle is (probably) the most ubiquitous principle in Physics, but who knows...