Except the cracking sound isn't Ganondorf's neck snapping back into place, since it just turns to look at Zelda, it sounds like it is breaking loose from all the petrification from however many years it's been down there. I still believe all this is just a call back to familiar scenes in past games for those of us enriched in the games and lore and nothing more. This would also be a big turn from Aunoma's comments about BotW being so far past all the other games they are just considered myths.