The problem in correcting it via this method, lies in the thickness of the flange. Having it plained for trueness might cure the issue initially, but you've now got replaced a flage that was previously very susceptible to warpage, with one that's even more susceptible. Since the metal is thin and there are no dowels to keep it in place, the header flange tends to move around with each heating and cooling cycle, which adds to the problem.
Your best defence against dealing with warpage is even torque across the entire flange.
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BBK's have a fairly thick flange, so my guess is that they're still probably pretty straight. The combination of a good gasket, high temp copper silicone and even torque should sort it out. I'd save any modifications to the flange as a last resort.