SOPs can never cover all eventualities. Sooner or later you will have to operate outside them. Logic dictates that you should get all input you can before making your decision, and you should then (if at all possible) brief the people concerned - FO, CC, ATC - whoever.
I would be disappointed in a company whose SOPs stated that the aircraft should be flown FD/AP on/engaged at all times. I would also be disappointed if they didn't stress that pilots should keep all their skills brushed up at all times - not just when the next Base Check is looming. Someone who doesn't know how to operate all the automatics in a skillful and professional manner is being as cavalier as the person who can't fly without them.
In the example given above, of the automatics taking you into harm's way, the fool who blindly allows the automatics to continue to do so will die a fool. Clearly that is not a case within the intentions of this thread.
Another point needs making - which is that, particularly at altitude, a human being, no matter how proficient simply cannot fly a modern high-performance aircraft as smoothly, as economically or as proficiently as the automatics can. Anyone who thinks he can is deluding himself.
There are right times and places to practise your skills and there are wrong places to do so. It is important not to get them confused. It is also incumbent upon us to keep all our skills up to date.