The combined efforts of all the fans beats what FJ was able to accomplish hands down, in terms of both quality man hours alone as well as access to materials. But that's because there are more of us and many of us have each devoted more time than he ever had; I'm willing to bet that's basically the only reason. Consequently, the output from fans tends to be more specialized.
Of course there will be shortcomings in the FJ tech manual; it was scrapped together after the fact. Since then, the fans have poured over the source material in efforts to correct the errors.
If someone like him, with a small team, had been hired to make the manual as the show was produced, it would have been more accurate; the TNG tech manual is definitely more accurate, although I'm not happy with its style.