I'm thinking that if the length of engaged threading were shortened, that the flange seating forces might do a better job of keeping the cartridge centered along the centerline of the shell.

Does a standard fixed cup sit square with the face of the shell? If so, perhaps the length of engaged threading or the thread's tolerances would explain the difference.

Another solution might be a cartridge bb with some thousands of miles on it already, or a cartridge bb where tilting forces might allow the cartridges to self-align to some degree.

Maybe it will be a cup/cone bb that ends up giving the most satisfactory service, or one of those cartridge bb's for use on threadless shells or on shells with damaged threads.

The use of piloted taps is something else that I might look into.