As someone who served (occasionally still, in reserves) in an infantry regiment of roughly 300 men, I seriously doubt whether any unit in this size can be effectively commanded by a single person. Even just the out-of-combat routine stuff like organizing a camp or resupply or checking to see everything's in order - that's just not possible without a clear chain of command down to the sergeant level. It just doesn't make sense politically and logistically, in terms of human organization - one person just can't take care of the numerous details one actually does need to take care of to get a regiment resupplied, or do basic training, or so on. In combat, my experience with a modern army, using long-range communications and weapons, may be quite different from an ancient unit's. Still, even if in theory possible having only a single commander would drastically lower the unit's tactical flexibility and capabilities: you can't divide the unit, or have an officer in charge of managing the breach while you lead the vanguard beyond it, or so on. In short, I find it extremely unlikely that Alexander was the only commander of a unit of 400 men, and would attribute such reports instead to the kinds of exaggerations that stories tend to. It may well have been that the unit could function in combat as a single unit under his direct command occasionally, but it'd still have sub-commanders that will start acting like ones when and if needed.
Regardless of the historical realities, however, Ars Magica strangely places very severe limitations on a person's capability to lead directly. In a "low-Mythic" game, I can see it working fine, as explained above, through chain-of-command. But even then, there certainly would be circumstances where the Leader can command many men at once! Ars Magica doesn't model this mechanically well, but I suggest the troupe can just allow them regardless - if the leader sounds his trumpet and all units rise from the ground and charge at once, that's fine; not allowing this because the order is supposed to go through a chain-of-command is just silly. However, the numbers do seem too low for a high-Mythic game; I'd certainly consider allowing Leadership to affect more men (Leadership! ? i.e. 1, 2, 6....) for such a game. Imagine the orc commander, personally leading a few dozen orcs.... yeah, that works quite well thematically, I think, even with no sergeants or such around.
Edit: It might help to think of the number of led-men as those in the general's staff, rather than the soldiers he commands. Still, a modern regiment commander can be expected to lead something like 11 officers, and I'd peg his Leadership as perhaps 6.