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If I put shield mods and/or armor mods as standard outfits, are they correctly added to AI ships? If not, then I have to manually adjust the shield and armor values for that ship? And if that's the case, the player will get the bonus without having the outfits if he buys/or captures that ship? So I'd have to make invisible "counteracting" outfits to cancel the bonus?
No, yes, yes, yes.
Use of përs neatly circumvents your problems, but only for specific ships. If you wanted a whole bunch of ships, that could get painful.