I'd argue that just about any fleet with a cruiser or better should allow for direct ship control. It seems a little weird that only with a perk or the highest commander in the entire chapter can you coordinate fleet actions.
From what I understand your average space marine isn't extraordinarily well trained in fleet combat. Of course they are all taught the basic tenants, but I imagine that outside of the chapter master, master of the fleet, and well-travelled company commanders they would stick pretty rigorously to the books. Besides, most ships are under chapter-serf command which presumably has its own hierarchy.
That's sort of a good argument. But chapter ships are often commanded by actual space marines, and being that that is their sole function I'd figure they would be not only good at commanding their own ships but large naval actions as well. Maybe it should be a threshold kind of thing. 5 ships or less = control. 6 ships or more = requires fleet perk or chapter master presence.
True that most ships are commanded by a space marine, or indeed, the full officer staff consists of space marines, but I imagine that after a point that becomes impossible before chapters start going far over their codex limitations (for the losers who abide that sort of thing anyways). Imagine, you've got a captain, executive officer, and lets say maybe three lieutenants? You start the game with like what, ~15-20 vessels? that's already 100 space marines, and imagine the more prestigious chapters like the Blood Angels or especially the Ultramarines, they've got to have 100+ vessels, no? A strike cruiser for each company, 2-3 battle barges, and at least 50 escorts. That's somewhere around 300 space marine fleet officers. Of course, if you have a space marine only filling the captain's chair that's still ~65 space marines, which might be doable for a larger/older chapter.
Of course, i'm not really sure if that's provided for in the codex astartes or not, all I found was the Space Marines are commonly officers.
EDIT: the point is, not ALL vessels are commanded by space marines. Furthermore, I find it EXTREMELY likely for the chapter master to defer command of the fleet action to the master of the fleet.