You are absolutely right in your example. Before his training he under-analyzed and thought a punch was just a punch, after his training he over-analyzed and thought a punch was no longer a punch, then after understanding it he simplified it and just analyzed. Bruce learned that a punch was just a punch, but at least he understood why it was just a punch, before then he didn't know that.
I think what Master Lee wanted us to gather from his unorganized quotes and insights, was that these were his thoughts and ideas, so they didn't really have to make sense to anyone else but himself. If one can't understand what he's saying, that's not a bad thing, it just means that they and Bruce Lee don't share the same ideology, there is nothing wrong with that. Bruce encouraged people to think differently and be their own person, that's the whole reason he created JKD, so he could set himself outside of the "classical" style of martial arts. While everyone was trying to fit into a set mold, Bruce Lee said "screw it" and made his own mold, that fit him perfectly. Now tell me that you wouldn't do the same thing?
Imagine that there was only ONE size of pants on the planet and you couldn't fit them. Now would you force yourself into the pants or would you take the time to make your own jeans that fit you perfectly? I took the same philosophies into consideration when I came up with Hip-Hopkido.
Think about it....