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I personally haven't seen much of an issue since the accuracy fix. I'll definitely continue to try to improve it where I can (I guess by looking on minimum elevation)...but if the AI decides it's going to shoot anyway despite the raycast being blocked I can't really do anything about it.
(apologies for late reply)
But look, there will always be a chance of turrets hitting your own ship depending on how things are designed...there is no avoiding that difficulty. That's why Keen implemented the no-self-grid-damage-from-turrets option, because it's no different with vanilla weapons.
The nature of weapons with lower projectile accuracy means that they have a higher chance of hitting the wrong target if you let the AI do all the work, cause the AI doesn't account for the accuracy at all.