Unfortunately you cannot add different damages on a single weapon. (That is, no engine damage+regular damage as in your example.) However, it might be possible to put several damage types on a mine, but I have never checked if it works. (A mine with a warhead doing damage to the engines, and another warhead doing regular damage)
Likewise, you cannot do something like the "Shield Nova" with the current code, as I don't think there is an effect draining the shields of a single ship (there is an ability lowering the shields for all ships in a given sector/system though, but that wouldn't work here). Boarding does lower your shields though, so it might be a solution with another purpose in mind.
Lastly, a single weapon cannot target multiple ships at once, although you could work around that by giving the Progen much improved Multiplex Targetting components, and smaller weapons, allowing them to attack several ships at once if they can do enough damage.
Good luck to you with this project, and the limitations of the current SE4. I am looking forward to playing such a mod, and will be interested by the results.
Re: Question for mainly you PBW/PBEM players :) (planning Earth and Beyond Mod)
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