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I have never heard of a FRED editor for OSX. Although you might be able to find a linux one. I haven't bothered looking.
It would be possible to have primary weapons fire 1 shot explodes in 1 frame, damaging the player (energy dmg only, no mass damage), and subs into the real, useful shot (which would pass through shields). This way shields could be used as a weapon energy bar. Of course, all "Useful" shots would need to pass through shields, and it raises the small problem of shields actually existing in FS2. Armor would need to self-repair as a result.
Also, how would we go about missions such as Bearbaiting, where you have to disable parts of a capship but not the whole thing? Could we use a bunch of planets and planet-destroying bombs? a few main undestroyable planets would represent the Sathana, and some small destroyable ones at the end would represent the beam turrets. After a set amount of time measured using a mission that is triggered when an invisible ship with a loooooong deathdelay dies, it would trigger the player to be transported to another system because the Sathana "jumped out"