I agree with John Tullamarine.It is impossible for SOPs to cover every eventuality. There are times when they are not appropriate to the situation and the captain must decide to deviate from them. This is an extreme measure and should only be done when there is no other option and when the pilot has sufficient knowledge to understand fully the implications of what he/she is doing. This is what command means. I can think of several examples.
Suppose on take-off at maximum weight in a four engine aircraft (a 747 with multiple landing gears) at a hot and high airfield, birds are ingested into both engines on the same side. Then, when airborne only a few feet above the ground, and barely able to climb, the co-pilot calls positive rate of climb, but the captain elects to leave the gear down until more speed and altitude has been gained. Non-standard, but his reasoning is that the extra drag of the open doors and wheel wells may well cause the aircraft to sink back towards the ground.
Suppose on final approach all engines suddenly stop. The captain elects to retract the flaps one notch. Non-standard, but the drag reduction is just sufficient to stretch the glide and make the airfield.
Suppose in mid-Atlantic, the underfloor cargo fire warning lights illuminate, the crew have reason to believe the warning is genuine and divert to the Azores. When they arrive the weather has deteriorated, the cross-wind has risen above limits and the cloud base has descended to below decision altitude. There is nowhere else to go and it is imperative to land. They do so successfully. All three examples were genuine events. It is not difficult to dream up other scenarios where such actions may be necessary.
And one more to ponder: the Qantas Airbus A380 at Singapore when the turbine disc exploded causing extensive damage and multiple unrelated warnings. In what order should the crew action the various procedures, which should be ignored and which have to be actioned?
Any serious captain should study his/her profession sufficiently so that he/she is prepared for such extreme eventualities.