I really don't see why the notion of Moltres taking more from Stone Edge is even being discussed tbh. The things that typically run Stone Edge, Tyranitar, Rhyperior, Gyarados, and fighting types, typically have other moves that will wreck both of them. In the case of the two comparable sets(SubRoost), Tyranitar handles them both with Crunch, as one defense drop means they lose. Most smart Tyranitar users won't even bother wasting their Stone Edge's precious PP, so in the case of the most used Stone Edger, irrelevant. Rhyperior has STAB Earthquake, so on a predicted Roost they will both lose. Irrelevant. Gyarados has STAB Waterfall for Moltres, and almost always runs DD, meaning Zapdos will lose if it tries to switch in(nobody would switch Gyarados into either of them for fear of Will-o-Wisp/Thunderbolt, respectively). Irrelevant. Fighting types typically don't run Stone Edge, but when they do, they are typically CBers or Infernape, so neither of these pokemon can defeat them. In general, Zapdos's smaller weakness to Stone Edge isn't something to gloat about, since both of them lose to the common Stone Edger. Sure, we could theorymon and come up with a pokemon that runs Stone Edge and doesn't have a STAB to combat it with, but that is not real.
The ONLY things hampering Moltres from being OU and replacing Zapdos are A)4x Stealth Rock weakness, and B)Lower speed, which to be honest the latter doesn't really matter since Zapdos uses that speed specifically for SD Lucario, while Moltres doesn't need the speed provided SR isn't up. So, yes, under normal battling conditions where SR is up, Zapdos is probably always going to be better, however, when SR isn't up, Moltres is nearly a clone with better characteristics, notably the fire typing which allows it to take on Heatran, the only pokemon that takes no damage from Toxic + Flamethrower.
EDIT: Zapdos only makes up for his stupid duck-like design with good stat distribution and typing. Even then, he is inferior to Rotom-A with the exception of the Pursuit weak, which is offset by the lack of a Stealth Rock weakness, and Will-o-Wisp.