The potential for mismodeling of νμ/νe, ¯νμ/¯νe, and νe/¯νe cross-section ratios due to nuclear effects is quantified by considering model spread within the full kinematic phase space for charged-current quasielastic interactions. Its impact is then propagated to simulated experimental configurations based on the Hyper-K and ESSνSB experiments. Although significant discrepancies between theoretical models is confirmed, it is found that these largely lie in regions of phase space that contribute only a very small portion of the flux-integrated cross sections. Overall, a systematic uncertainty on the oscillated flux-averaged νe/¯νe cross-section ratio is found to be ∼2 and ∼4% for Hyper-K and ESSνSB, respectively.