Think of it this way... Your engine is providing a constant pull on the carbs depending on RPM. If you're at idle, the only thing that the vacuum effects is your pilot jet, because it provides the least resistance to the pull. As your RPM increases, the pull increases. This causes more air to be sucked into the mixture, and the carbs compensate by moving up to the next step in jetting, the slow jet (which provides slightly more resistance than the pilot jet). Now keep in mind, the pilot jet still continues to allow fuel to pass, but the slow jet is making a "correction" to the fuel/air mixture.
As you continue up in RPM, the same thing happens again. At a certain point, the slides begin to move and the main jet needle (the next step up) becomes involved. It's tapered, so the farther up the main jet holder it goes, the more fuel it allows to pass. This is why the clip is important... A lower clip setting and you allow more fuel to pass from the get-go since it stations the needle farther up, while a higher setting allows less to pass since you're stationing the needle closer to the orifice (it's like sticking your finger into a hole in the bottom of a boat... take your finger farther out and it allows more water to get in). And when you're at 3/4 to wide open throttle, the main jet itself becomes the major player, and its size determines the mixture at that throttle setting. But remember, at WOT it's not just the main jet that's providing fuel... the pilot and slow jet are also still in the mix, they've just been "overtaken" by the correction to the mixture.
So, to get back to the original question, changing the clip on the needles will only affect the mixture at a certain RPM/throttle setting. Doing this for an exhaust change MAY be sufficient, because a new exhaust won't necessarily affect a particual area of the mixture. However, if you make the change to pods it will affect the airflow across the entire board, and you will have to change pilots, slows, main jet needle clip position AND main jets.
Understand now?