We present an in-depth study of the universal correlations of scattering-matrix entries required in the framework of non-stationary many-body scattering where the incoming states are localized wavepackets. Contrary to the stationary case the emergence of universal signatures of chaotic dynamics in dynamical observables manifests itself in the emergence of universal correlations of the scattering matrix at different energies. We use a semiclassical theory based on interfering paths, numerical wave function based simulations and numerical averaging over random-matrix ensembles to calculate such correlations and compare with experimental measurements in microwave graphs, finding excellent agreement. Our calculations show that the universality of the correlators survives the extreme limit of few open channels relevant for electron quantum optics, albeit at the price of dealing with large-cancellation effects requiring the computation of a large class of semiclassical diagrams.