Not specifically Moltres, but I had an idea of how to only encounter them once. You don't get and attack in, but you still send out your Pokemon if I remember right. Would using shadow tag stop them from fleeing? Thanks!
It is impossible to battle the roaming birds on the first turn, even Abilities such as Shadow Tag will not keep them from fleeing, you must encounter them 10 times before you have a chance of catching them.
Unlike previous roaming Pokémon, the birds will automatically flee seconds upon encounter before the player gets a chance to act (Abilities such as Shadow Tag will not prevent this).
Source
