Jeff that's an interesting note about Mr. Dye. Now that I think about playing his courses, while the surrounds are often very difficult I never felt I was presented with an unfair shot while on the green.
But then there's 6 at Whistling Straits, which may be the poster child for this type of conundrum. And to your last paragraph's point, it's a hole where your approach should be from a short enough distance that it's not too much to ask the player to hit the correct portion of the surface.
Generally, I think good design differentiates between players of different abilities, provides recovery options that are more easily unlocked by the more skilled player, and rewards good positioning. If that means leaving the possibility that a player could get so out of position, even while on the green, as to need to pitch the ball if they want a tap-in for their next shot, I think that's okay. In real life, I've only ever tried to chip from a green once (on 10 at Tobacco Road), so it's not like this is some architectural scourge. And I 3-putted twice just yesterday, so it's not like this game owes anybody a tap-in for every second putt.
Even for a very skilled player, pitching from a green involves taking some risk. A less skilled player might well find that taking their medicine, lagging a putt to 12 feet or so, and then trying to make the next one gets them down in 2 more often, and virtually eliminates the "4s or more" that the player who tries to pitch brings into play. How is that situation any different than any number of others that arise in the course of play, where the aggressive recovery player can take some risk to try something heroic while the more conservative player can mitigate risk by setting sights on the more reliable but less spectacular option?
Granted, my club's superintendent would probably disagree with me.