In many cases...
In many cases, if you look in the preamble of both the FCOMS and your company's SOP, there is a 'disclaimer'. In many cases, the airline is assuming liability for deviation in its SOPs from prescribed procedures set forth in the manufacturer's FCOMs.
However, in some cases the NTO exists.....Single-engine taxi might be one example of this.
In all cases, what we do and how/when we do it is specifically and explicitly approved by FAA. Example, a normal checklist: Our company had its own normal checklist, which was different from the manufacturer's.
At the bottom of our checklist was a signature of the POI (Principal Operations Inspector....or the specific FAA office charged with overseeing our operation) approving that checklist.
This practice is common in the U.S. Most large air carriers have their own way of doing things. Right, wrong, or indifferent....smart or stupid....that's the program.
In my case, I never cared one way or the other....just tell me what you what, and that's what I give you. Pay me at the end of the month, and life is good. I always looked at the SOPs as a security blanket. It's difficult to hang me in a court of law when I was following my company's SOPs (that were approved by the FAA).
In point of fact, legally, I would be in violation to not follow the SOPs.
Each air carrier, in order to obtain an air carrier operating certificate, must jump through many hoops as dictated by the regulating aurhority. One hoop is that the carrier must have prescribed, approved, operating procedures, some sort of flight operations manual, etc. Following those procedures is the basis of certification.
Fly safe,
PantLoad