Superb post Pixy, and for my world view, right on the money, however...
As a lowly "unable to form an opinion unless its given to me" F/O here at EK a few things stand out regarding letters, fuel tables etc etc such as this.
First things first, its their train-set, sure you assume responsibility when you accept the aircraft and dispatch etc, but its their train-set, so for me, regardless of professional pride, ego, experience and all those other loaded words, the fact is they own the keys to the things, so I play by their rules.
Secondly, whats wrong with asking for a new flight plan if your not happy? just make sure you can justify your query/request.
If guys are so concerned about getting a letter that questions your decision making, then perhaps that shows a lack of maturity when it comes to being able to accept that everything we do is analyzed from the comfort of Costa and its done of course with the singular benefit of 20:20 hindsight.
Guys like TCAS exist everywhere, they thrive in a rule based environment, they derive satisfaction from observing the normal amongst us squirm and pontificate when we are in essence put on the spot regarding our decision making process and outcome.
The great thing about all this rule based behaviour is that its completely self serving and manageable, i.e. use the rules to your own advantage, not theirs.
I won't expand any further on that purely because why should I help the rule makers make my life harder? but if you don't want to feel under-pressure, think a little more laterally when it comes to how rules are applied.
As an example, I used to fly with a guy in a previous airline who whenever he carried more than plog fuel he made sure to fire off an email to anyone who would listen as to why he did it, sure it pissed a few off, but it created an audit trail, and it showed beyond any reasonable doubt that he had considered his decision rather than say throwing on 4 tonnes "for the wife, kids, girlfriend etc"
Like I said, I'm a lowly F/O, I couldn't possibly imagine how galling it is to have your decisions and even your authority questioned.