The distinction is not essentially vacuous: it's possible for the learning of "how to do independent research" to be itself largely independent, e.g. Edison and Einstein.
I said I don't recall Larry talking about this anywhere - can you show where he does? Specifically, about how doing the PhD helped this specific person to learn to do independent research. I'm interested in this.
Maybe a nod is encouragement, but it sounds like Larry had decided to do it anyway - so the statement reads as an absence of discouragement.
On reflection, I think we mean the same thing, your "learned a lot from his advisor and other graduate students", and my "great people around him". There's a question of what a PhD is. It could be the independent work; the academic justification and presentation in terms of literature; the discussions with smart, interested people. (btw I've been doing one for a few years now).
I think our disagreement is about our definitions.
Seeing as one major focus of a PhD is to learn to do independent research, this statement is essentially vacuous. It also disregards the influence on his thinking process from his advisor (Winograd) and fellow graduate students.