Points per mission have a rubber banding effect depending on your overall placement (ignoring brackets). This means that if your score is lower than the average for the position that you're in, your missions will be worth more compared to others in that same position. IE, if Bracket Alpha's 1st place has 750 points and Bracket Zeta has 500, Zeta's 1st will gain more points from missions to equalize brackets. This will filter down to lower ratings as well, since naturally in that case, 50th would necessarily be lower in Zeta compared to Alpha. This has the effect of allowing brackets to push higher as a group to achieve the further out rewards.
Phantron wrote: You only have to play your last set of missions after whoever is in the lead overall. Of course the later you wait the better off you'll be, but generally speaking the guy who is in the lead overall has no reason to wait until the last minute to play his mission (because he's still #1 no matter when he finished them, assuming nobody was able to beat more missions than he). The only thing playing early is getting you the illusion that you're placing well. That is, if you play say 7 hours before it ends, after you're done you'd be like #10 and you think that's pretty good, and by the time the tournament ends you'd drop to about 100. But, if you waited until the very end, you'd still only finish around that range, though you wouldn't see your rank drop for obvious reasons.