Hello David,
I have to disagree with your first statement, so I will give you a professional opinion(as an engineer).
An intercooler is basically a heat-transfer device, and maximizing the delta-T(change between inlet and outlet) will increase it's efficiency. Any 'medium' or buffer that stands between that transfer reduces the delta-T(and that includes paint, regardless of how thin it is. Think of sleeping on a summer night...blankets are like coats of paint on your body. Thick...not so good when it's hot. Thin sheet, much better. No sheet, and maximum transfer of your heat to the surroundings.
Now, if we remove that paint off the stock intercooler, there will be some increase in efficiency(hence more power), but is it significant? I would estimate at maximum boost, maybe tops a 0.75-1.0% increase(2-3 HP). To be more qualitative, VERY controlled testing would have to be done to validate that number, but I'm confident it would be in that ballpark.
An aftermarket, direct replacement will not only cost money, but typically will create more turbo-lag, and will require a different turbo to get the same flexibility/drivability out of the motor(and I want the present system to be seam-less, as I have virtually little or no lag with my present 3.3L...

).
I'll provide pic's once it's done.