I also understood your question to be about a stock system, and your wanting to shortcut a performance mod.

In your case (and Banks), what likely happened is their intake with the MAF relocated (originally) was decreasing the OEM efficiency of the MAF. Relocating (correcting) it likely replaced what was lost, and it is again more efficient and within its operational window. Taking it outside of it's operational window will wreak havoc with the PCM, as Banks discovered.