There are a number of advantages AND disadvantages. Its not for everyone.
Many people have installed cams, exhausts systems, etc, on the L-Jet EFI cars and it becomes a real compromise. Tuning out the flat spots, keeping fuel economy, and so on, becomes a real chore (if not flat out impossible). The most obvious benefit to this strategy is being able to take advantage of your modifications with ZERO down time.
As far as the AFM and TPS are concerned, I'm 'ignoring' both of them. A vacuum line to the ECU is all that's necessary for load and acceleration enrichment (replacing both the AFM and TPS). Yes, you'll get better response if you use an actual pot. style TPS, which is why I wired up the 3 existing TPS wires so that you may add one at your leisure. Then its a simple matter of telling the software to use TPS instead of MAP for transients. Currently, the MAP based transient response is about on par with stock.
The idea is to provide a means of growing the system to meet your needs or wants over time. Even adding a turbo wouldn't be unreasonable... all the remaining Wolf features are still there to take advantage of, as the individual chooses.