The electromagnetic properties of neutrinos, which are either trivial or negligible in the context of the Standard Model, can probe new physics and have significant implications in astrophysics and cosmology. The current best direct limits on the neutrino millicharges and magnetic moments are both derived from data taken with germanium detectors with low thresholds at keV levels. In this paper, we discuss in detail a robust, ab initio method: the multiconfiguration relativistic random phase approximation, that enables us to reliably understand the germanium detector response at the sub-keV level, where atomic many-body physics matters. Using existing data with sub-keV thresholds, limits on reactor antineutrinos millicharge, magnetic moment, and charge radius squared are derived. The projected sensitivities for next generation experiments are also given and discussed.