I understand that the states are related via a unitary transform between the two pictures, but the outputs (like population, photon number, etc.) are expectation values, which should be the same regardless of the transform.
In the interaction picture, the energies of the atomic levels are not fed into the code, so the results won't depend on them. However in the Schrodinger picture, the energies are present, and have influence on the results. So to me there seems to be contradictions. Please point me out if I'm wrong about anything.
Thanks!