It appears to have no bearing on it whatsoever however if you have any prior bans in regular competetive, the next ban up will occur for comp CTF (So say you had a 2 hour ban in Comp, you would receive an 8 hour ban from CTF if you left 1 game of CTF)
Found it out from a friend whose connection seems to short circuit. It's not much of a big deal overall but if it occurs early in a match he gets a ban for it which we noticed added to CTF despite him rejoining within less than 5 seconds.