Those are all great questions. On the last part, you lump Akagi in with Kaga and Soryu, but her fires were different, more like Hiryu, not like the other two at all. Kaga and Soryu were hit and their hangers had, literally within seconds of the attack, blown apart along the lengths of the ships. Akagi's fires, like Hiryu's, were much slower to become out of control, such that even an hour later they were hoping to contain the blazes. On Soryu, "her damage had been so rapid and severe, and the slaughter of her crew so wholesale, that only cursory efforts were made to save her." On Kaga, "The condition in Kaga's hangers immediately after the bombing were horrific beyond description". But on Akagi, "Near at Hand, Soryu was heavily afire.....Kaga <was> burning furiously. Yamaguchi tried to make out the situation on Akagi. She was still steaming northward. To the bridge watch he announced that the flagship was still proceeding at good speed and her damage appeared to be slight".
The hit on the rear edge of the central elevator was right on top of the B5N2's stored on the hanger deck below, but unlike in Kaga and Soryu, they didn't chain detonate. Akagi's fires took a while to get going, and unlike this pair, her total killed were much lower, (267 killed on Akagi, similar to Hiryu's 392, far less than Kaga's 811 and Soryu's 711). The theory is that the reason why Akagi burns like Hiryu and not like the other two is that Soryu and Kaga had all their aircraft in the hangers, and they went off in a chain instantly killing hundreds on the spot, while Akagi's were not in the hangers and burned on the flight deck where they did less damage and killed fewer people.
The Akagi had only 68 mechanics killed to Kaga's 268 and Soryu's 242. I don't know how many mechanics there were per aircraft, but including 6th Ku passengers, that translates into -
Akagi - 1.13 mechanics killed per aircraft
Kaga - 3.72
Soryu - 4.24
So Akagi had far fewer mechanics killed per aircraft than Kaga or Soryu because her launch status was different. The reason why the mid-ship hit did not set off a hanger chain-detonation starting with the B5N2's right below the blast is because those Kates were on the flight deck, not in the hanger. That's the theory, at any rate.