I think your points are generally on target and that taken together, they add up to what I'd consider the truth about those three courses. There are not tons of difference in quality among them in terms of the actual routing and design, each has its strong points.
What puts Pine Needles above the other two in my estimation is a combination of two factors. What you describe as
Generally, the more difficult set of greens, but not necessarily the most charming or creative.
is something I'd describe more strongly. For my game and the games of the guys I've played the courses with the greens at Pine Needles are quite challenging while looking very benign. Maybe the green complexes there just fall in some kind of "sweet spot" that gives me just the amount and kind of challenge that I crave. Southen Pines has a few interesting greens but Mid-Pines has a mixture of a few outstanding greens with some that are very mundane. Whichever hole is the short Par 4 with the green situated up and to the right and some cabins or lodges down below the right side of the green (3rd?) is perhaps better than any green across the road but there are at least 6-8 completely unmemorable ones.
The second factor is conditioning. The two trips I've made to play these courses (two rounds at Mid-Pines and four at Pine Needles IIRC) have found tight, muddy lies on offer at Mid-Pines including for wedge shots. Maybe I just caught it on two bad days but having to hit wedges off bare or thin muddy ground is a huge minus that I simply never experienced at Pine Needles. And of the three courses the bunkers and greens were more consistent at Pine Needles, too. I hate to sound shallow but I enjoy dry and firm turf more than getting mud on my trousers.
So on balance, all three courses have very good designs and a great feel to them. All are great walks by modern standards, admittedly Mid-Pines takes the prize in that area. And I love, love, love the green complexes at Pine Needles which is enough to put it what I've referred to as "all-World" status in my book. The other two courses come up short by way of a few weak greens and occasional poor turf.