Well because of several things, the time he spends fighting the covenant that coensides witht the training of Spartan3s, the lack of mention of Akherson at all, (it even mentioned Dr. Halsey at some point in the series) Not to mention the very end of the book saying that hes going to finally become the soldier that everybody needs him to be in order to lead the war against the covenant. I dont think that going undercover and training spartan 3s that never even are heard of by anybody is really 'the fighter everybody needs him to be'. It seems almost aparent that Johnson spends the most of his time in engagements or in cryo. Also dont forget in The Flood it says that Johnson spent many many years just traveling on and across planets.