If I recall, BANKS is more than just "messing" with the MAF. It is just part of the whole equation in how it relates to the engine management system (stock or not) that creates "more power." Since, I do not know about the Banks system you are talking about it is hard for me to get specific as to why/what they are doing. Although, knowing Banks kits, I would assume that it is more involved then just moving a stock MAF to a better place - although I could be wrong.

Easiest analogy I can think of help you. On a gasser with a distributor. The factory sets a specific timing that is realiable, dependable. You can gain a few HP (5-10 depending on motor) by advancing/tweaking the timing. Advance too far and you get denotation and pinging. Take that to MAF, you can gain some HP by tweaking it tricking the motor to squirt more fuel. However, tweak too much and you get driveability and computer issues.