Looking at the manual for a 6442 controller, I expect both focus pens are wired to the same LimZ- or LimU- pin: the first pen to hit the material sets the focus position. Although there are two laser control outputs, there does not seem to any provision for independently moving the two heads in the Z (or U) axis.
So I think the two heads are intended to operate at the same focus height.
You could defeat that by setting this head at a different, ideally higher, point on its mount, so auto-focusing the other head puts this one at the right height. It wouldn’t be convenient if you had short jobs with different heights for the higher head, but if you’re running production you could use a step gauge to set whatever offset you need for each material at the start of the run.