I created a mutator that does some ModifyPlayer() stuff, and it works excellently in Deathmatch and Team Deathmatch. Upon trying it in Vehicle CTF, though, I found that it did not do anything that it was supposed to, and putting a `log() entry in ModifyPlayer(), I found that the function wasn't even being called.
Doing some scouring, I found that ModifyPlayer() is called by SetPlayerDefaults(), which is a gametype function. In Vehicle CTF, this function is overridden to set the class of the player's hoverboard, but it does not call super.SetPlayerDefaults(), so ModifyPlayer() is never called either. I would imagine that this is not the intended functionality, and so I wanted to mention it for discussion or for some head people to read and see "oh, crap, *fixfixfix*".
And for clarification, adding "super.SetPlayerDefaults();" in at the end of the SetPlayerDefaults() function of UTGameContent\UTVehicleCTFGame_Content.uc fixes the issue.