measured both, at 48KHz, for you. rockboxed x3 vs stock x3.
stock (unloaded and with Pai Audio MR3 -multiBA-): rockboxed (unloaded and with MR3):
comparison, stock vs rockboxed, with MR3 (big format, to distinguish details; click on the image):
about tonality, both are flat, and rockbox version stands a bit better with highs (so it shouldn't sound darker at all). but some slight ripples appear along the whole frequency range.
noise, distortion, etc. look very similar, but there are slight differences which i don't know to interpret (and maybe the differences are due to different measure conditions/parameters); together with the ripple in frequency response of the rockboxed version, it could tell about slight clearness in stock version (but it goes beyond my limited knowledge).