Wouldn't the panel also have to be listed for its intended use ? If a 200A MB panel comes from the mfr. with the capability of 40/80 circuits, they put it through UL and had it listed that way. I'm sure some type of calculations were done during the design stage to limit the # of breakers that could be installed with a 200A main. Changing that main to a 100A would violate the UL listing IMHO. I know (logically speaking) that irrespective of the amount of CB's you install after changing over to a 100A main, the max the panel can deliver is somewhere in the area of 100A.
My point to all this is, if MBP's were intended to have whatever size main CB's installed why not sell them separately that way. Have a 40/80 MB panel sold (without the MB) and pick whatever size MB you want off the shelf. In fact, why not have a 80/160 panel avaiilable. The same principle applies.