Now looking at the pictures above, I would think that the fitment of the exhaust flanges would mate to the surface of the header's face/surface. Is that correct?
Incorrect. The header actually seals on a copper (or at least I think it's copper) gasket inside the exhaust port on the head. The flange where the bolts go through is there to apply clamping pressure to the header where it fits inside the exhaust ports. If you look at the last inch of the header where it goes in to the head you'll notice the diameter of the pipe increases. That's where the flange presses aginst to hold the header tight aginst the head. The gaps should be even on every flange.