What you have seen there is a perfect demonstration of the result of 'Elastic Foundation Theory', you can Google it, it's not BS. The bolts bend the flange and induce a wave in it which is why there is a 'best' tension for the bolts. It is a serious issue for large bolted or rivetted stuctures, but with welding far more common these days it is less commonly experienced than a century ago.
You have number of options, but the central issue is to get a stiffer flange, the rolled edge seeks to do this - poorly. Adding bolts halfway between the existing ones effectively does this since the centre distance between the bolts is halved. The bending of a beam is proportional to the square of its length so you would expect a significantly smaller deformation with twice as many bolts (I won't say a quarter because there are other issues to be considered). However, if you were to add a backing ring to thicken the flange, beam bending is inversely propotional to the cube of its thickness so you would get a lot more extra stiffness that way.
It depends on what the mating flange is like, it may not be practical to fit a backing ring to that, 'though two semi-circles may be a possibility. If you try to go too thick with the seal to accommodate the undulations of the flange(s), there is an increasing risk that it will just blow as a result of the internal pressure
Richard
