I am taking the free action of the 3 eye attacks in any one 90 degree arc can be used then face downward thus putting a 90 degree arc and cone of antimagic ray down the shaft.
Aiming all three eye attacks downward is but one of many options. You can aim them forward, backward, left, right, up, down. To aim the antimagic ray, he would also need to tilt towards the shaft, which is another free action. He can do all of that during his round if he pleases.
So that question is answered though not sure if you are saying he can do that because of Flyby attack or because it was a free actin to pan or tilt.
Its a free action. The text says he can tilt during his round. Tilting is not an attack. He simply adjusts his facing.
The question that was not answered is reaction and initiative. The Beholder moved after the PCs as they ascended upward in the shaft magically. I asked when he looks downward with his anti magi ray and engulfs them all, and none of their flying or darkvision items work, does the effect happen right then and there so they get a reaction to it plus their initiative before the Beholder goes again or do they fall on their initiative?
The moment the Beholder hits them with the anti-magic ray, that is when they fall. So it happens during the Beholder's round.
Whether you allow them to react to it is up to you. You can rule that they get a Reflex save DC 15, to grab hold of something. Or you can rule that they immediately fall down and take damage. If the players have items that require only a free action to activate, then I would allow that, even if its not their turn yet. Of course a ring of feather fall isn't going to do much good while they are still inside the anti-magic effect. But any free action, which can be done in a split second, should be possible. As a DM you can make rulings whether an action that the players want to attempt can be done as a free action, or requires a full action. When in doubt, use common sense. Falling happens really fast, so they have to react in a split second.
We have the same issue when in the middle of battle the Cleric turns undead. Do they run then or can other players strike on their initiative and then the undead run on their initiative?
Movement takes place during the turn of the creature. Hypothetically, if the creatures were to run during the round of the cleric, then what happens when its actually their turn? Do they move again? That would effectively give them double movement. So the answer is, no, they move when its their turn. But you can tell the players that the undead react to the spell and are repelled.
Effect and Duration of Turning
Turned undead flee from you by the best and fastest means available to them. They flee for 10 rounds (1 minute). If they cannot flee, they cower (giving any attack rolls against them a +2 bonus). If you approach within 10 feet of them, however, they overcome being turned and act normally. (You can stand within 10 feet without breaking the turning effect—you just can’t approach them.) You can attack them with ranged attacks (from at least 10 feet away), and others can attack them in any fashion, without breaking the turning effect.