max,
I could be losing the plot a little bit here!
I think theres a little difference between rules of the air vs management expectations, and the aircraft manuals.
As far as A/C operating manuals are concerned, on the FAA side, at least, any company holding an operating certificate must have all manuals, procedures, etc, detailed in the company operations specifications.
This document varies from company to company, and is approved/disapproved by the FAA based on company history, type of operation, equipment, facilities, personnel, etc.
The operator normally uses the manufacturers manual as a guide for their aircraft, and modifys to suit their needs. The outcome is that whatever rules, etc, contained in the particular company Ops Specs becomes law, despite what may or may not be in the original handbook. As I said, this will vary from company to company!
Generally not a problem, because straying too far from the manufacturers ideas will mean the FAA will not approve!
The accepted 'rules of the air', on the other hand, are just normal procedures used by everyone who flies, not only laws, but also general 'customs' developed over time.
I thought you were referring to issues like duty time, rest periods, etc. Often, for logistical reasons, the company will push the crew to fly one more leg, or a few extra hours, beyond the customary or mandated duty time. This is where the crew are caught out!
Refusing can shorten their employment prospects with that company, but agreeing, and flying the extra, can get them in trouble if anything goes wrong!