In case you didn't know: If the first Pokemon in your party has Synchronize, wild Pokemon have a 50% chance of having the same nature as it. This is the other affect Synchronize has, as well as sharing status ailments.
But I was wondering, would this still work if I were to put a Pokemon with Synchronize at the front of my party and I encountered a legendary Pokemon at the stage of the game when you find it? Because it wouldn't really count as a 'wild' Pokemon, as its not in the wild.
And also, if it does work, and I was doing this for the roaming legendary bird encounter in X/Y, at what stage would I have to put the Pokemon with synchronize at the front of my party? When you first find it, or when you can first catch it?