Kyle,
You have much to learn. While Flynn was very attentive to par 3s and may have been as good as any designing great sets of them, Rolling Green gets the overall nod in my book among Philadelphia Flynn courses and just may the equal of Shinnecock Hills.
As you suggest, Rolling Green is much better than Manufacturers in the long par 3s. 10 and 14 at Rolling Green are superb and nothing comes close to them at Mannies. The deception on 3 and the setting on 16 are at least the equal of the short holes at Mannies, even though 8 is a very fine hole. 6 at Rolling Green is very good and may be the only par 3 at RGGC that is not the equal of any at Mannies, but not by much.
Consider the par 3s at Shinnecock. Wow! I guess I have to give the edge among Flynn courses to my favorite course in the world. 2, 7, 11 and 17. Forget the template holes of Macdonald and Raynor. These natural sites (OK, Flynn raised the 7th and it is not natural--but it is great) blow away most every par 3 that I have personally experienced. 11 is the greatest use of a natural ridge site for a par 3 hole I have ever seen. Wait till the tee is lowered to its original height and the forward tee moved back to the left. It'll be even better with the sklyine effect that will be returned.
As regards Shinnecock Hills, right on, Sully! Indian Creek are hard to hit as well. Something about those perched greens on Florida courses and the wind.