The stern planes are set for dive as I understand it and I'm not convinced the tube inner doors are that weak at that depth, even if a DC exploded close which is not indicated by any damage on the starboard bow. I would believe that with the forward ballast tanks damaged from the port side detonation, she was unable to rise. I saw nothing to prove the people tank was breached and flooded so I don't know why they believe water got in. Subs do not have much buoyancy reserve, like a surface ship, so ruptured ballast tanks are enough.

Anyway that's my take.

EDIT: After reading diving procedures, I see that the stern planes are used for controlling the "bubble" or angle. Diving fast in shallow water you would want to keep close to zero bubble so as to prevent plowing the bow into the seabed. The planes would be as they were found like this.
stern (\).........bow(\)

I was referring to the outer torpedo door being partly open, which it was. The inner door was closed, but that was the only reason I can think of as to why the outer door would be half open or half closed and there being no torpedo inside. E.G. it had just been fired and was in the process of being closed.

As for the dive planes, generally speaking on a US sub, the bow planes control the depth and the stern planes control the dive angle. The normal procedure for diving is to set the bow planes with a downward angle on them and to lift the stern, an upwards angle is set on them, however much you want. As the axis of rotation of the sub is about the conning tower, which is about one third of the length back from the bow, as such, the stern planes exert a much greater leverage on the sub than the bow planes do. They are also directly behing the props, so they have even more influence. If you were to try to dive with the stern planes set hard rise (e.g. bow / stern /) then the stern would sink faster then the bow and it would be pointing upwards.

The external ballast tanks would all have been flooded - a sub cannot dive with any of them filled with air. Rupturing an external ballast tank would have no effect on buoyancy, but the damage to the pressure hull where it was stoved in would have and would have caused her to be heavy by the bow.

Perhaps this is one for DaveyJ's thread?

The ruptured ballast tanks would prevent any possibility to surface again, or hold depth for maneuvering was my thought. I agree ruptured tanks would not greatly effect a sub already in a negative buoyancy trim, but would certainly effect any control thereafter had they any time left. And I do think at least some aft compartments would not have been flooded by the limited visible external damage. Anyway, we will never really know.