One point Lyons does not make is that the brilliant team that kept the ship running smoothly while he was gone were all recruited personally by Jobs. I've written before that recruiting brilliant people may be Jobs single most important skill. I am sure that Apple will need to continue to recruit brilliant people in the future in order to sustain its current level of success.
The point Lyons makes about all of his contacts, emails, etc. on his new phone before leaving the store should not be underestimated, either. This kind of thing is part of the culture of near-insane attention to detail established by Jobs. Apple comes close to removing the fear of learning, configuring, and migrating to a new piece of technology. There has always been a certain nagging dread of what can go wrong when updating to a new Windows OS. Even if its better than what you have now, the expected pain leads to putting off the purchase. It might be possible to sustain this culture without Jobs, but I and other Apple shareholders don't want to find out.
Lastly, I do not think this is true of only Jobs, but founders in general. I don't think Microsoft is the same company run by Ballmer as it was under Gates. Without Jobs, Apple became the definitive case study of how a company can still lose with superior technology. (I know there are other examples of companies losing what made them successful when the founders left, but I'm drawing a blank on remembering them right now.)