Shell
You are right. Very often he said "RAF" when it should have been "MoD". The same applies daily in the press and here on pprune. The RAF fly, RN sail and Army march. But his meaning was clear as witnessed by the MAA being pan-MoD, not just RAF or Nimrod.
However, the evidence presented to him did show that the systemic problems (as opposed to isolated cases) commenced in anger with RAF decisions, mainly by suppliers, when they took over the world in the late 80s. That makes his 1998 baseline all the more bizarre and, lacking any other evidence, I have always thought this a "deal" whereby MoD knew they had to take a hit, and agreeing to 1998 protected many retired officers. His reasoning was so ludicrously flawed it took about 30 seconds to find the written evidence that proved him wrong (which had been submitted to him anyway).
As I've said elsewhere, his naming of General Sam Cowan (Ret'd) was particularly unwarranted as senior RAF officers before him (1987 - 1994 in particular) had deliberately wasted vast amounts which knowingly targetted airworthiness; whereas the "cuts" Cowan was accused of making were miniscule by comparison (5% per year for four years, against almost 30% a year for 3) and had little effect. And, having met the man, I know he was particularly concerned about these fundamental Duty of Care issues. H-C was a force for good, but a lot of very senior people breathed a sigh of relief when they read his report.