It is likely IMHO that EACH BH is warped along the edges or somewhere in the body when off the engine. I suspect it all comes from how to machine the cast BH in the first place. That open flange ('free face' I'll call it) of the BH that goes against the block is just naturally more prone to warping and flexing since it is open, relatively unsupported, and widely spread. It makes no sense to machine the trannie face, bolt/clamp that to a reference surface, and then machine the free face while not torqued to anything, because the free face IS gonna move off 'somewhere' when torqued down. Machine the 'free face' (block face) first, bolt/clamp that down to a reference surface which moves/distorts the casting to its final form as it will be when bolted to the engine block, and then machine the trannie face parallel to the reference surface. An interesting manufacturing problem....