Can I join this from a point of the intelligent layman?
I have 5000 hrs Helicopters, mostly SAR.
The question I come to is ,was the FMC a formal limit, or just advisory info?
If it is a limit, then your captain is not justified in exceeding it unless life is at risk, which I seriously doubt in a 747 at FL410 cruise.
If it is advisory, then you possibly need to find a way of asking your captains to explain themselves to you.
This is like defensive driving in a car - you are not at fault but you need to manage others so that they do not put you in an awkward position. Not being an airline pilot I bow to your brothers in the business at this point as to how.
I would say that you are absolutely right to raise the issue and talk it through and if your captain and company won't you have made a brave step raising it here.
I'll fly with you any day.
Sven