Has anyone thought to look for the flaperon everyone thinks was on 9M-MRO? This sounds silly, it would certainly represent an appalling lapse in the keeping of maintenance records, but if that is in fact the flaperon from 9M-MRO with an incorrectly documented modification then MAS's record-keeping isn't exemplary either. Do they have any other B777's with documented modifications as they appear on the recovered item?
Another thought centers around how the ID plate came off. It is quite possible that it corroded away to nothing, and is in solution in the Indian Ocean. Otherwise, I imagine whatever Boeing uses to bond ID plates to components can survive solvents, detergents and thousands of thermal and pressure cycles, it seems unlikely that seawater alone would penetrate and break it down completely. On the other hand, if the plate had been removed and reattached previously (there have been cases in the past where components that were allegedly scrapped have been rebirthed) the bond could be less than perfect. Come to think of it, are all MAS's (in particular) flaperon ID tags correctly attached?
On the whole, I think the most likely explanation is that the flaperon is the genuine part that was fitted to 9M-MRO when it disappeared and that MAS's record-keeping isn't up to standard. On the other hand, the proof is not absolute, and so far the French investigators have reported enough discrepancies that some other possibilities can't be ruled out. I don't believe global conspiracies or alien (or CIA) abductions played any part in this mystery, but there seems to be some dubious maintenance practices in play. "How dubious?" remains the question.