EVERYWHERE I've ever worked, the SOPs over ride the AFM/POH
In every OM I wrote or worked under, the OM stated clearly that where there was conflict between the OM and AFM/POH, the AFM/POH information had precedent.
This was to cover a couple situations where a third party not familiar with the AFM/POH published conflicting information in the OM or the AFM/POH was amended that put the OM in conflict with the AFM/POH.
The only SOP that I know off that was against the AFM was in one company who flew a mixed fleet of fixed gear and retractable gear aircraft where the undercarriage up and down calls were standard across the fleet.
And that's why CASA changed the laws about 20 years ago to "Accepting" rather than "Approving" Ops manuals. They shifted the legal burden away from themselves to the AOC holder and pilots.
For over 40 years the only part of an OM requiring approval was a CAR217 Part C.
One crucial bit of the approach in QF1 that the ATSB missed and did not comment on, which would have prevented the accident, was during the approach where one of the crew stated, during the investigation, that the runway was only visible to the crew directly behind the sweep of windscreen wipers. I believe that it is a requirement for the runway to be continuously visible to the crew when continuing the approach below the DA.
If they had conducted a missed approach when the continuous visibility requirement was lost, we would not be talking about this today.
Anyway this is completely of topic.
Back to the B200. Auto-feather is there for a reason, especially with Raisbeck 4 bladed props. Use it. End of story.