Oh I study the R/V Petrel images quite a bit when they came out, including some you likely didn't see. The torpedo tubes you are referencing are the FORWARD tubes between the stacks, not the aft tubes. A substantial portion of the aft deckhouse was found laying upside down by Petrel. The three aft 5-in gun mounts were also found by Petrel. The 5-in mounts were a key factor in identifying the wreck that Petrel found was USS JOHNSTON (DD-557) and NOT USS HOEL (DD-533). JOHNSTON had the gun captain hoods only on mount 55. USS HOEL had gun captain hoods on mounts 51 53, 54, and 55. Only one of the three 5-in/38 gun mounts located by Petrel had a hood.
The three images below provide the addition proof that the midships photo shows the forward torpedo tube mount and NOT the aft torpedo tube mount.
The first overhead image of USS JOHNSTON shows her final configuration. The thicker line drawn over the ship is roughly where the ship broken into one major section (bow and bridge) and the aft section that broke into multiple pieces. The two circles show from where on the destroyer sizable pieces of the wreck that Petrel found were located. The mounting ring for the AFT torpedo tubes and the forward section of the aft deckhouse with the aft torpedo reload crane recognizable even upside down. Please note the feature I have an arrow pointing to. This is a shielded deck hatch to the engine room below. There were NONE of these aft of the twin 40-mm wing mounts. The use of this shield was common on SeaTac built units.
In these two screen grabs from Thursday's discovery, note that where that shield is located. So in effect the arrow is pointing toward the bow. Also, to the left of the first image, above the end of the torpedo tubes, can be seen the FORWARD torpedo reload crane.
Also, in this view that shows a bit more of the deck below the twin 40-mm mount, if this was the aft end of the deckhouse, at least the wreckage of one of the 20-mm guns should be visible.

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Nope right back at you.
The problem is that the Petrel found an area around the torpedo tubes, specifically the catwalk area, leading from the after deckhouse to the tubes that appears to be there on the new imagery. So... either the Johnston sprouted all new torpedo tube mounts and deckhouses or the wreck that the Petrel found WAS NOT the Johnston.
The Johnston and Hoel were only separated by a few miles when they sank, and these were positions taken in the heat of battle, so they were subject to error. USNA work using Heerman's last reported position for Hoel places Johnston relatively close to Hoel's last reported position. Remember, Cmdr. Evans went off on his own, and Johnston's positions were sporadic and open to interpretation. We could be looking at two different wrecks relatively close together. We just don't know. Further surveys of the Johnston's wreck may glean more information. 'Til then, we just don't know quite what the Petrel found. A Fletcher? Certainly, but which one? The amount of debris, including the huge amount of debris from deckhouses, gun mounts, etc., indicates that it may, just may, have been the Hoel. With the absolute greatest of courtesy, match up the debris the Petrel found with what remains of of the Johnston. Watch the videos. You'll see what I mean.