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Cosmic rays (CRs) with ~GeV energies can contribute significantly to the energy and pressure budget in the interstellar, circumgalactic, and intergalactic medium (ISM, CGM, IGM). Recent cosmological simulations have begun to explore these effects, but almost all studies have been restricted to simplified models with constant CR diffusivity and/or streaming speeds. Physical models of CR propagation/scattering via extrinsic turbulence and self-excited waves predict transport coefficients which are complicated functions of local plasma properties. In a companion paper, we consider a wide range of observational constraints to identify proposed physically-motivated cosmic-ray propagation scalings which satisfy both detailed Milky Way (MW) and extra-galactic $γ$-ray constraints. Here, we compare the effects of these models relative to simpler 'diffusion+streaming' models on galaxy and CGM properties at dwarf through MW mass scales. The physical models predict large local variations in CR diffusivity, with median diffusivity increasing with galacto-centric radii and decreasing with galaxy mass and redshift. These effects lead to a more rapid dropoff of CR energy density in the CGM (compared to simpler models), in turn producing weaker effects of CRs on galaxy star formation rates (SFRs), CGM absorption profiles and galactic outflows. The predictions of the more physical CR models tend to lie 'in between' models which ignore CRs entirely and models which treat CRs with constant diffusivity.