pg might be interesting again if he said what "unsayable" and "aggressively independent-minded" things he actually wants to say, and I wish he bloody would - we've got no choice but to read it.
"independent-minded" is such a cliche now - it's often a euphemism for something else. Surely more truly "aggressively independent-minded" people are homeless addicts, not rockstar founders. What's the right balance between conformism and independent-mindedness? In what areas of life? This 2-axis system is way too simple. Start there, dude.
By implication pg (and YC) recognise and value independent-mindedness - but as you say, from the outside YC appears to reward conformism to their well-understood creeds (as well as just playing the odds of an enormous number of companies, rather than being clever pickers).
(edit: removed snark, however deserved)