Can you enlighten us on this intriguing mystery?

Sorry, not really. Either looks plausible. All the dictionaries I checked derive métier from ministerium and not from mysterium. You'd really need to talk to a French lexicographer to find out what's up. It's good to remember that the etymologies one finds in dictionaries are just an abbreviated form of what scholars write out in articles and monographs which would contain more of an argument for why a certain etymology lost out to another one.

Ceci n'est pas un seing.