You're only part right, Mooga. You lose any sensitivity [toggles and buttons] support if you use a Joy2Key type of application. I think that if you want to remap any buttons with TF2 and the 360 gamepad support you need to edit the config files, but any other game that natively supports a 360 gamepad will normally accept in-game remapping.
So you're right that it's easier to customize in some cases, but the gains far out weigh that point when we're talking native support.