To return the unvignetted ARF the source position needs to be forced to be the position of the optical axis. This can be achieved by defining it in telescope coordinates.
arfgen spectrumset=spectrum.ds withsourcepos=yes sourcecoords="tel" sourcex=0
sourcey=0 filterdss=no withdetbounds=yes withbadpixcorr=N modelee=N
detmaptype=flat detxbins=1 detybins=1
This returns the on-axis effective area with no PSF or bad-pixel correction.