I haven't read the whole thread yet, so I'm sorry if this has been responded to, but as a native local and the bay being my old stomping grounds that the deepest part of the bay is the channel. Where the burning ship is is right outside of the channel. The channel is right outside of the containment booms you see floating out in front of the bow. The channel runs parallel to the coast at that point, and would probably be (without breaking out my charts) the only part of the bay that would come close to being able to swallow a ship like that. That would block all large traffic to the southern part of the bay.
Active Captain has the Navy slips at 32 to 37ft. Ship draws 29ft. Say the deck is 29 ft above water(just a guess), they would have to find 55+ feet of water to get it below water.