$Subsystem: {name}, 0, {value}
?I tried "damage as hull" and the subsystem was immune to weapons that damage subsystems only, however it was not immune to other types of weapons and eventually it got destroyed. Assigning 0% of the parent ship's hitpoints should and adding the "damage as hull" flag should indeed make it invulnerable and not a damage sponge.
Okay, than that is just switching the damage calcuation from "{actual damage} = $Damage: (https://wiki.hard-light.net/index.php/Weapons.tbl#.24Damage:) * $Subsystem Factor: (https://wiki.hard-light.net/index.php/Weapons.tbl#.24Subsystem_Factor:)"1 to "{actual damage} = $Damage: (https://wiki.hard-light.net/index.php/Weapons.tbl#.24Damage:) * $Armor Factor: (https://wiki.hard-light.net/index.php/Weapons.tbl#.24Armor_Factor:)"1
1 - incomplete model, real calculation might have addtional factors
But I am glad that it works.
As for the roation issue - do you have a before and after of the table entry you can show us?
$Name: UEF Kentauroi
[...]
$Subsystem: intaker,15,2
$Alt Damage Popup Subsystem Name: Intake
$Flags: ( "untargetable" )
$animation: triggered
$type: Afterburner
+delay: 0
+reverse_delay: 1000
+relative_angle: -11.40,4.68,-0.50
+velocity: 11.40,4.68,0.50
+acceleration: 11.40,4.68,0.50
+time: 2000
[...]
$Name: UEF Kentauroi
+nocreate
$Subsystem: intaker,0,2
$Alt Damage Popup Subsystem Name: Intake
$Flags: ( "untargetable" )
$animation: triggered
$type: Afterburner
+delay: 0
+reverse_delay: 1000
+relative_angle: -11.40,4.68,-0.50
+velocity: 11.40,4.68,0.50
+acceleration: 11.40,4.68,0.50
+time: 2000
$Name: Vulcan
$Damage: 500
$Damage Type: NormalWeapon
$Armor Factor: 1.0
$Shield Factor: 0.0
$Subsystem Factor: 0.0
vs$Subsystem: communication, 20, 0.0
$Flags: ( "carry no damage" )
$Subsystem: sensors, 20, 0.0
$Flags: ( "damage as hull" )
Result: communication wasn't destroyed but the hull was damaged, sensors was destroyed (couldn't tell if the hull was being damage when the subsystem was still alive, hence test 2).$Name: Vulcan
$Damage: 500
$Damage Type: NormalWeapon
$Armor Factor: 1.0
$Shield Factor: 0.0
$Subsystem Factor: 0.0
vs$Subsystem: communication, 0, 0.0
$Flags: ( "carry no damage" )
$Subsystem: sensors, 0, 0.0
$Flags: ( "damage as hull" )
Result: The hull was damaged in both cases.$Name: Vulcan
$Damage: 500
$Damage Type: NormalWeapon
$Armor Factor: 0.0
$Shield Factor: 0.0
$Subsystem Factor: 1.0
vs$Subsystem: communication, 20, 0.0
$Flags: ( "carry no damage" )
$Subsystem: sensors, 20, 0.0
$Flags: ( "damage as hull" )
Result: The communication subsystem was destroyed, the sensors wasn't.