arfgen provides two ways to improve the consistency when fitting multiple instruments.
The parameter applyxcaladjustment instructs arfgen to apply an energy-dependent correction function to the output ARF of the MOS cameras such that spectral fits will be cosistent with those of the EPIC-pn camera. Details of the derivation process of the correction array can be found in CAL-SRN-0382.
A correction for all of the EPIC cameras to bring returned fluxes into line with a perceived "absolute" flux value, as derived from spectral fits to data from other X-ray missions can be applied using the parameter applyabsfluxcorr.
These corrections can be applied independently or together.