It seems that a Manual J can at best only be a very rough estimate, because it's so hard to take good account of roof ventilation.
I got my roof ventilated a few years ago and it cooled down my house like 10 degrees during the day. It made a BIG difference, and a lot of difference in how much AC would be needed. If I didn't care about dehumidifying I would barely need AC at all.
I don't know whether the Manual J normally takes any account of roof ventilation. Contractors doing such estimates probably aren't getting up there and trying to figure out out many sq in of exhaust ventilation you have, or whether insulation is blocking the soffit vents, or measuring the temperature in the attic.
Asking people how hot a house gets without AC would be an important input that also may not be part of a Manual J? My answer to that would have been very different before and after getting my roof ventilated.