For what it's worth, my mentors said the same thing about Pete's earlier work, like Harbor Town. Their thought was that the bunkers laid flat, not sweeping up like a MacKenzie (or Jones Sr.) bunker, etc. The Harbor Town greens were little plateaus, with not a lot of contour (because they were small).
They felt like he had a hard time thinking out of plan view. Of course, they had no idea of his love for Langford greens, etc.
It had nothing to do with working on flat sites vs. rolling ones. Of course, Pete's designs, whether via his evolution or that of his growing number of associates certainly evolved over time. I also recall them commenting on PGA West being way over shaped. Specifically, some of the shaping was so far from the greens, i.e., two rows of backing mounds/earth forms. They asked why he would do it. My response was, "Uh, it looks pretty spectacular!"
In the end, you have to remember that Dye got a lot of criticisms from the old line architects when he got successful, just as Doak, CC, etc. get now. What's funny is if RTJII thought criticizing work of others would lead to more work for him (it won't, never has, never will) you think he would pile on the current crop of hot architects. Him critiquing Pete is like the Republicans going back in time to pillory Hillary, when they should be focusing on the current opponent.
(Just MHO and an example, not a political statement.)