I agree it comes down to individual airlines' SOPs.
Boeing does recommend using both APs for all approaches.
If SOPs dictate otherwise it could be for many reasons that FOPS decided this course of action, old habits or being unfamiliar with the alternative being one of them.
Flying an approach dual channel on an average day is not a problem, as most pilots revert to hand flying no later then say 500'. The missed approach issue as discussed would be aided by automation in these cases.
As long as it is recognised that there is a trim issue below this, crew are aware of this and brief accordingly when weather minima dictate this may happen, there appears to be no issue.
Protected runways are only required for less then Cat 1 weather, thus this does not prevent crew using dual channel to minima and even let the aircraft land when Cat I minima exist on an unprotected runway.
Change the SOP, use the automation, or be prepared for some handling incidents when crews are caught out having to fly the missed approach manoeuvre manually late on in the approach.