Piggy Back controllers allow stock ECUs to do things that they normally can't do, like run larger injectors or deal with boost. Remember that piggyback controllers work by altering sensor signals before they get to the ECU.
Most of the time, the primary signal being messed with is the Map Sensor. This is critically important in a Speed Density car. The Map Sensor is used by the ECU to guess how much air is going into the car, and therefore how much fuel to supply in order to match airflow. When you "lean" out a car with an AFC, you are simply decreasing the Map Sensor signal - the ECU responds to the decrease in manifold pressure by supplying less fuel. When you "richen" a car with an AFC, you are simply increasing the Map Sensor signal - the ECU responds to the increase in manifold pressure by supplying more fuel.
The change in fueling happens for a reason: if you look at a fuel table, Map Sensor values correspond with columns. When you increase or decrease the signal from the Map Sensor, you are simply making the ECU use a different column than it originally would have used. (see Understanding Maps if you need some help understanding reading Fuel and Ign tables)
But wait, isn't the Map Sensor used for determining ignition requirements too? When you "lean" out a car with a Piggy Back, you also in all likelyhood advanced timing. When you "richen" a car with a Piggy Back, you also in all likelyhood retarded timing. Look at trends horizontally (as MAP changes) in an ignition table, and you will see why this happens. This helps explain why so many boosted cars running on the "AFC hack" have issues due to excessive ignition advance.
The bottom line: Piggy Back Controllers suck because you cannot independently adjust fuel and ignition. Any changes to fueling will produce a change in ignition too, and often this is undesirable.