well an aftermarket cdi does more than just raise the rev limit.. a good one will also smooth out all the peaks and valleys in the timing curve creating a smoother power flow balancing it all out, making for nice smooth power building up all the way to the new red line; so your power doesn't fall off short of redline.. this is where all your supporting mods come in such as intake and exhaust. think of it this way, your engine is nothing more than an air pump. the more air you can pump in the more air you need to pump out. hence if you increase the flow of air intake the need to add a higher flowing exhaust increases to pump out the larger volume of air. but now you cause a lean condition in the cylinder so you need to add more fuel to compensate and richen the mixture, this is where jetting comes in. this all causes a need to ignite the mixture at a different time depending upon where you are in the rpm range and how much throttle is aplied and how much load there is on the engine to produce an efficent spark to fire in the cylinder which causes more horsepower.. you see horsepower is a byproduct, a result, not the cause. and this is why an aftermarket cdi box is neccecary once you reach a certain point in your modifications which is also why you see stage 1,2,3 cdi boxes, each one is designed for different stages of modification... stage 1 for simple mods such as basic intake and exhaust, stage 2 for when you go beyond basic and add a cam and possibly a larger bore, and finally stage 3 for when you decide to get really wild and add some head work such as porting and polishing and maybe some bigger valves to flow way more air both in and out and a really agressive cam.
stage 1 would be for fun trail riding, stage 2 for agressive trail riding and some racing from time to time, and stage 3 for all out racing.
hope this sheds some light on things and helps to explain more, what a cdi box does and how to properly choose the one you should be getting for your needs, and why/when you SHOULD be getting one.