if the raised welds were perfectly round and to the exact size of the gasket, i could consider taking your word for it. but the fact of the matter is that in some places on the flanges, the welds are 1/4" wide, and in a lot of places, they are 1/8" wide and some places even less than that. so the gaskets would have to basically be perfectly placed around the header to get a good but still uneven seal.
by making a flat and level surface, it ensures a more uniform seal on the gasket around the exhaust port. therefore more evenly distributing the exhaust gas pressure on the entire ring. furthermore, by smoothing out the hard edges of the weld going into the tubes, allows for better airflow. if i owned a flowbench, i would test it out, but rounded edges are better then sharp edges any day.
i know for a fact that the flanges of the joe z exhaust on my car are perfectly flat, and have the same type of gasket you provide for connection to the exhaust system.... which are full flanged sized gaskets, meant to seal the entire surface area not a tiny 1/8" wide rim around the inside.
back to the header, since there will be no metal to metal contact, due to the thickness of a gasket being in between. my flat and even surface would seal with the exact same force as your raised welds, given that the gasket itself looks to be around 1/4 - 3/8" wide around the exhaust ports. again, with the varying width of the raised welds, some parts would utilize 1/8" width of the gasket and even less in some places, that is a pinched gasket.
and as for my "eyeballing" of straightness. before and after comparisons, as well as numerous checks during the hand filing, using multiple straight edges and a machined flat piece of metal on a table saw would confirm that the header now is closer to flat then it was with the raised welds. also, the files themselves are perfectly flat, or else what use would they be. i have 8 hours into working on this one side, as little metal as possible was taken off. each port is perfectly flat around the diameter of its opening.
now i'm done ranting, im not going to argue anymore, because i know that i just made a good product, better, and probably more reliable.
just for fun, use the internet, and search for header flanges, 99% of them have flat faces, with no raised points for "sealing" the gasket. case closed.