I just tested the IQ4 with latest firmware with my XF (also latest firmware) and the auto ISO appears to work fine. The 16 bit vs 14 bit capture bug is still there with both the XF and with no body (tech cam use), however.
Speaking of auto ISO, the nature of the IQ4 sensor's dynamic range means that Phase One should really be using 1/3 stop auto ISO increments, rather in full stop increments. Indeed, the auto ISO values used by the XF (see http://photonstophotos.net/Charts/PDR.htm#Phase One IQ4 150MP) are actually the worst "bang for the buck" ISO choices— the best being 1/3 stop BELOW each full stop (so ISO 160, 320, 640, 1280, 2500, 5000, 10000, and 20000).
Speaking of auto ISO, the nature of the IQ4 sensor's dynamic range means that Phase One should really be using 1/3 stop auto ISO increments, rather in full stop increments. Indeed, the auto ISO values used by the XF (see http://photonstophotos.net/Charts/PDR.htm#Phase One IQ4 150MP) are actually the worst "bang for the buck" ISO choices— the best being 1/3 stop BELOW each full stop (so ISO 160, 320, 640, 1280, 2500, 5000, 10000, and 20000).