The two parts have unrealted functions.
The TRE does what it's called, Timing Retard Eliminator. It makes the ECM think it's in fifth all the time, making the fuel injection mapping use the fifth gear mapping full time. In the case of the 2001, it removes the top speed restriction, but it can't unrestrict the 2002's. Also by mapping the fuel injection to fifth, it eliminates the under 4000 RPM lurching and surging.
The power commander lets you alter the fuel injection maps themselves, by altering the signals that the FI controller sends out. This is important when using aftermarket exhaust systems.
By using the two together, you end up with a single fuel injection mapping for all the gears, which is a little easier and less time-consuming than re-mapping all 6 gears on the ECM itself. If you unplug the power commander, it goes back to stock, unlike remapping the ECM, for which you need a dealer (or possibly a Yosh box) to do.