Just and educated guess here, but from installing a 3 point SB on my 02, any factory equip STB mustangs would have had the notch removed (from the plastic shroud), by the factory. All you are doing is creating a metal to metal mating surface (also so you can drill into the fire wall for the bolts that will hold it).
I personally think the STB is a good upgrade for our cars (corning feels much tighter). Everything I have done to my 02, I have done so with trying to maintain a very stock feel (as if it came from Ford this way). Once installed the area you have to notch is almost completely unnoticeable.