If you go back to the 1960s/1970s during CPL training there was much emphasis on the responsibilities and legalities (Air Law) of being an Aircraft Commander (how often is that term used these days? - one usually hears the term "Captain"). How much emphasis does CPL training these days give to the responsibilities of being an aircraft Commander?
Since then we have seen a continual eroding of the authority and respect shown towards the Aircraft Commander from various Operators. Whilst I am in favour of CRM and the like we seem to be breeding aircraft "managers" these days.
There are occasions when the person in charge (especially where lives are on the line) has to have the moral courage (aka b***s) to do the right thing (= leadership) as opposed to doing "things right" (= management). This would include (but not be limited to) the carriage of fuel above flight plan. This would also include going against the (Company) "party line" (in the sense of applying a greater margin of safety).
In a Company which I once flew for significant changes in procedures were announced which, in my opinion, were more to do with concerns to do with who would get the blame if anything went wrong; these procedures were, in my opinion (and those of other pilots I talked to), less "safe". I was flabbergasted that the pilots were never consulted about said changes. With CRM Commanders are encouraged (rightly) to consider fellow crew member's views on operational decisions, yet it would seem the Company had the attitude of "we know best" QED