Well there a lot more people who notice more whistle than those who don't.
That is the reason Ford installed it after all. The Early 99 trucks don't have foil on the intercooler pipe. They installed it on the hot side pipe in the late 99's and up to reduce the noise in the cab. They also changed the compressor wheel on the turbo to accomplish this. There were complaints about the turbo noise in the cab. This is how they fixed it.
As to your exhaust...That has no effect on this. Removing the foil from the pipe does not increase the whistle out the exhaust. It will only increase the whistle you hear in the cab. Your exhaust is probably loud enough that it drowns out the sound a little so you can't tell as much of a diiference
Like Kevin said, this is not really a 'mod', and it will do nothing for your truck except clean up your engine compartment and increase the whistle in the cab.