I'll load up Sub Command in the morning and take a look at it. All you should have to do is set up the ships so they're on different sides and then make the rules of engagement "Wartime" for each side that you want to fight. There have been some instances of AI ships not attacking certain things in Dangerous Waters (Oil Rigs... but that's fixed with the Sakura Mod and a little bit of a workaround). I'll take a look and see what happens when I set something up in Sub Command.
If you want, you can email me a copy of the scenario and I'll take a look at it.
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