My opinion of what might have happened...
That was the best documentary ever made of the Fitz. It's what made me obsessed with Great Lakes wrecks.
That animation gives me the chills, and its just as likely to be the cause as my theory.
Were they not able to determine that the ship snapped in two from the wreckage? I suppose sound vessels with watertight bulkheads needn't sink due to "merely" breaking in two, but whatever the cause, the cards were heavily stacked against her for multiple reasons.
@craig61a answered this well. His animation shows one way the ship (boat, they're boats on the Lakes) may have broke and sank.
I think it broke on the surface, suspended at either end by two monster waves. The boat had a history of bending and flexing in odd, unsettling ways, and every captain and engineer who sailed it had something to say about it. One former chief engineer is on tape explaining how he demanded the owners look at and fix the problem, or the boat would sink. I think he even threatened law suits, or to go to the CG. This, combined with overloading and hard sailing makes me believe the boat broke on the surface. None of the other 10 or 11 boats on the lake that night sank...
Both of these theories make sense while looking at the wreckage and how the cargo is scattered on the lake bed. What doesn't make sense is the Coast Guard's official reason, that the hatch covers were leaking. It seems to be a classic CYA answer, as it absolves the Coast Guard (who allowed the Fitz to sail overloaded and certified her as seaworthy when she had obvious issues) and ship owners and operators (who deferred maintenance wherever possible and encouraged heavy sailing) of any responsibility. The families never accepted that, though. They knew their guys were good sailors and wouldn't head into a storm with hatch covers not dogged.
We'll never know, as diving on the wreck is effectively banned after they released footage of a body lying down there.