Joe,
I feel you are assuming that the size of the putting green, and the size of the "pinnable and holdable" areas of the putting green are one in the same when they are not necessarily.
Keep in mind that my argument is based on "larger greens" that fit with the surrounds and not necessarily large greens that are arbitrarily placed. The greens in question were initially this size, only to shrink due to any number of factors including budget, incompetence, or both.
In the case of a hole like 15 at Manufacturer's, 6, 7, 8, 10, 11, 13, and 14 at PSU White and the 8th hole at Huntingdon Valley, green expansion has/could allow for hole locations to he placed on the periphery of flat areas, bring surrounding contour features into play, which when mowed as green or even fairway provides a stiffer challenge for both the short game and approach shot, since a misstruck shot is more liable to run into trouble and in a more awkward situation.
This is hardly categorical, and all depends on the blending of bunkers, greens, fairways and contour through maintenance - but if the joints are there, larger greens can provide, in my opinion, a more complete challenge.