I have noticed that loop corrections to both the CC and NC MSW matter potentials are available in the literature by now, see Phys.Rev.D 108 (2023) 9, 093010.
As discussed in this phenomenological follow-up study investigating DUNE's sensitivity to the NMO and deltacp, in the case of the electron (anti)neutrino CC potential, which is the only relevant one for standard three-neutrino oscillations, this correction apparently amounts to +2.0% when the potential is expressed through Fermi's coupling constant (as we do in prob3 here).
At the very least, in my opinion we should allow users to choose to apply the above NLO correction to the CC potential in prob3 and look into, if necessary, updating the CC and NC potentials in the PISA-compatible nuSQuIDS branch.