Yes BOAC is right, Captains discretion can certainly be used prior to the first sector of a flight and it definetaly is not a "means to get you home that shouldn't be used to depart from your home base if its use will be required". That permission is clearly granted by the wording. If the commander elects not to utilise it thus, that is entirely up to the commander.
Anti ice your statements are rather vague in that I cannot see how a commander would impose discretion on you so that your ( and some of your colleagues) duty hours were "illlegal". Such a situation could only come about if there were extenuating circumstances concerning your (and their) particular duties. In which case it was incumbent on you to notify the commander of the circumstances prior to the start of that particular duty.
As BOAC has already pointed out the limit is only reached ( except in situations that the captain deems an emergency) when the the relevant FDP and any discretion provided by the rules that the captain chooses to apply has been reached. You should ordinarilly report for duty sufficiently fit and rested to be able to comply with such a requirement. The rules provide for flexibility and are not quite as "cast in stone" as you would like them to be, nor is the legality compromised by the use of Captains discretion as you suggest.