We're talking here about rewarding smart flag play, when much of the discussion is smart defensive play.
I'll say this - in the most recent playtest, a teammate of mine had grabbed the flag at the first stage I believe, and as he went out into 0g, he was killed and the flag drifted out towards the opposing team's starting base and I followed it a little. An opponent came along and sat right next to the flag and waited for me to come close, it took a short while for me to get close enough to kill him with the weapons I had, at which point he then returned the flag. By this point, he was not alone, I was unable to kill him, I died and the flag remained safe; had he returned straight away, I could've just turned back and grabbed it, with a headstart, too. Smart. Defensive. Play.
I think @InevitablShenanigans is just talking about the challenge races, right?
The idea of those is a competitive mini-game between matches and also offline, so varying player stats based on routes would be a bit counter-intuitive I think, but I can see where you're coming from with the logic.
@Lightningy - I think getting points for taking the flag from the stand is completely reasonable, and perhaps you could also add a capped 'time holding' point system as well, so that if you just grab and die you get little, but if you grab, make it out but die on the way back, you still get some points for the effort maybe. I personally don't care about personal points, but team points need to be balanced very carefully.