We aim to investigate the influence of the eccentricity and inclination damping due to planet-disc interactions on the final configurations of the systems, generalizing previous studies on the combined action of the gas disc and planet-planet scattering during the disc phase. Instead of the simplistic $K$-prescription, our n-body simulations adopt the damping formulae for eccentricity and inclination provided by the hydrodynamical simulations of our companion paper. We follow the evolution of $11000$ numerical experiments of three giant planets in the late stage of the gas disc, exploring different initial configurations, planetary mass ratios and disc masses. The dynamical evolutions of the planetary systems are studied along the simulations, with emphasis on the resonance captures and inclination-growth mechanisms. Most of the systems are found with small inclinations ($\le10^{∘}$) at the dispersal of the disc. Even though many systems enter an inclination-type resonance during the migration, the disc usually damps the inclinations on a short timescale. Although the majority of the multiple systems in our results are quasi-coplanar, $∼5\%$ of them end up with high mutual inclinations ($\ge10^{∘}$). Half of these highly mutually inclined systems result from two- or three-body MMR captures, the other half being produced by orbital instability and/or planet-planet scattering. When considering the long-term evolution over $100$ Myr, destabilization of the resonant systems is common, and the percentage of highly mutually inclined systems still evolving in resonance drops to $30\%$. Finally, the parameters of the final system configurations are in very good agreement with the semi-major axis and eccentricity distributions in the observations, showing that planet-planet interactions during the disc phase could have played an important role in sculpting planetary systems. ; Comment: 13 pages, 14 figures, Accepted for publication in A&A