This review paper emphasizes the significance of microscopic calculations with quantified theoretical error estimates in studying lepton–nucleus interactions and their implications for electron scattering and accelerator neutrino oscillation measurements. We investigate two approaches: Green’s Function Monte Carlo and the extended factorization scheme, utilizing realistic nuclear target spectral functions. In our study, we include relativistic effects in Green’s Function Monte Carlo and validate the inclusive electron scattering cross section on carbon using available data. We compare the flux-folded cross sections for neutrino-carbon scattering with T2K and MINERνA experiments, noting the substantial impact of relativistic effects in reducing the theoretical curve strength when compared to MINERνA data. Additionally, we demonstrate that quantum Monte Carlo-based spectral functions accurately reproduce the quasi-elastic region in electron scattering data and T2K flux-folded cross sections. By comparing results from Green’s Function Monte Carlo and the spectral function approach, which share a similar initial target state description, we quantify errors associated with approximations in the factorization scheme and the relativistic treatment of kinematics in Green’s Function Monte Carlo.