Context. The gamma-ray emission from Starburst and Starforming Galaxies (SBGs and SFGs) strongly suggest a correlation between star-forming activity and gamma-ray luminosity. However, the very nature of cosmic-ray (CR) transport and the degree of their confinement within SBG cores are still open questions. Aims. We aim at probing the imprints left by CR transport on gamma-ray and neutrino observations of point-like SFGs and SBGs, looking into quantitative ways to discriminate among different transport models. Moreover, following the reported scenarios, we quantitatively assess the SBGs and SFGs contribution to the Extra-galactic Gamma-Ray Background (EGB data) and the IceCube diffuse observations (HESE data). Methods. We analyse the 10-year Fermi-LAT spectral energy distributions of 13 nearby galaxies with two different CR transport models, taking into account the corresponding IR and UV observations. We generate mock gamma-ray data to simulate the CTA performance in detecting these sources. In the way, we propose a test to discriminate between the two CR models, quantifying the statistical confidence at which one model can be preferred over the other. Results. We point out that current data already give a slight preference to CR models which are dominated by advection in their nucleus. Moreover, we show that CTA will allow us to firmly disfavour models dominated by diffusion over self-induced turbulence, compared to advection-dominated models, with Bayes factors which can be as large as 10 7 for some of the SBGs. Finally, we estimate the diffuse gamma-ray and neutrino fluxes of SFGs and SBGs, showing that they can explain 25% of the diffuse HESE data, while remaining consistent with gamma-ray limits on non-blazar sources. Conclusions. Our results point out that future gamma-ray telescopes such as CTA and SWGO will constrain the high-energy emission from nearby galaxies, thus providing remarkable insights into the CR transport within SFGs and SBGs. In particular, they will potentially confirm these sources as efficient high-energy neutrino factories contributing to the diffuse neutrino flux.