There really is no explanation for the Pillar of Autumn. Shoot the mystery bridge is the least of the level’s problem since the incredible Warthog Run, while incredible, tells you to drive 3 times the length of the ship in an almost straight line.
Also while EckhartsLadder brings up some good points that are smart and good, he’s missing one key factor.
You can kick the Flood’s ass with energy swords. But Star Wars has laser swords. Lasers. QED.