The thing is 98% of FULL ISO's have had the Update removed (where possible and not gamebreaking). Unless you're getting UMD dumps and scene releases you're not getting the FULL game, although no-one would dispute an image lacking the update folder (and consequently smaller) is still complete.
You've also got the fatmsmod.prx which governed MS access. Sony changed this from 3.80 (inclusive) and up so that every firmware after 3.72 had slower data exchange rates. Dark Alex later solved this by showing us that this prx could be flashed into later firmwares, and then went one better in 5.00M33-6 by incorporating the ubiquitous MS Speed Boost.