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3.6 is a Custodian update with no associated DLC. The Custodian team does a release every quarter, the Expansion team does not.
Re: Rationale for Torpedoes dealing extra damage to large ships:
We have a strong precedent for not explaining every detail, so you can create your own canon. Like how we don't explain exactly how your FTL drives work, this is a case where I'd prefer to leave some room for personal interpretation.
My own interpretation is similar to that of some of posts in this thread - torpedoes either blow clean through smaller vessels, or their explosions somehow react with the greater mass of the larger ships, perhaps somewhat like the Molecular Detachment Device from the Ender's series. Different empires may have different mechanisms for this.