The problems mentioned aren't specific to diving. Take martial arts, for example. I've seen "masters" of forms who have never been in a fight. Technically, they are very sharp and IN THEORY should be able to take care of themselves. On the other hand, I know a fellow who is still rated a white belt (rank amateur), but the only way I'd want to be in a fight with the guy is if he's on MY side! In other words, he could probably wipe the floor with some grand masters, but he doesn't have any recognized standing.
We could make the analogies and expose the pitfalls of the current certification systems all day (and sometimes folks here on the board do just that), but it doesn't fix the problem--it usually only winds up in a comparison of different agencies with many folks beating their chests and proudly proclaiming "MY agency is better than YOUR agency". That gets old in a hurry.
Bottom line seems to be: If you want to earn the Master Diver designation, do so. The courses are designed to be enlightening and fun, and they're another excuse to go out and use up a tank or two of air. Who knows? You might even learn something. But the unspoken caveat is "don't wave the cert in another diver's face, because he/she might very well be far more experienced and skilled than you are." And don't think because you have the cert that you have no further need for training and/or experience. Like one of the popular mags says..."a good diver is always learning." Get out there and dive and have a good time learning as you go.