I really dont know whats haywire with the OEM tune that causes the failure.
I think that when Cobb comes out with the AP, the tainted MS3s who need to adress the recall still, will not have to worry with the AP tune, it should write over the OEM tune to the extent that its as effective as doing the recall flash since Cobb will have rewritten all the timing and fuel tables. Now, when somebody with the tainted car pulls the AP tune, he best have the Mazda flash lined up really soon.
With a good tune, the MZR should run for a very long time as long as Mazda R&D'd the motor well enough to withstand high miles. There are many old turbocharged Subarus still on the road, so I dont think our turbo motor will age too badly.
Pre-ignition is a silent killer. Often times, you cannot detect it. Its different than detonation, much different. Pre-ignition starts as the piston is on its way back up, but early during this stroke. As the fuel is now buring as the piston is traveling upward, the piston heats up and the rod is stressed. Broken rod, or blown piston, neither are much fun. Any motor can suffer from this if not tuned properly. the error is in Mazdas factory tune. Now, as to why Mazda tampered with a perfectly good tune, I dont know.
With all that said, with the proper tune and maintenance, the motor should last a long time if its not beaten on, just like any other quality motor (you know, some motors are just garbage from the beginning).
Fuel pumps dont usually slowly die. If this were the case, there would be many, many engines that suffer a pre-ignition death. As motors age and tolerences loosen, they arent nearly as sensitive to imperfections. Cylinders will lose compression, oil may leak through certain seals.