Of course the big problem in buying an expensive black paint M3 is that you dare not use it because it is so valuable. And although a black paint custom job may cost as much, the intrinsic value is less if anything happens to it, so it's not like an appreciating asset or anything is it.
But a paint job is a more complicated thing than many people expect. The chrome has to come off the appropriate parts, the painter has to understand how to paint (which many don't, especially 'have a go amateurs'), and they need to be able to put it all back together with some mechanical sympathy. That is why it is expensive, and unless the donor M3 has already 'paid for itself' it really can be nearly as expensive as buying an authentic camera.
Steve