Internal damage is technically still hitting the armor, and keeps all its resistance stats. Armor penetrator causes a negative damage resistance debuff that massively increases damage to armor. Because internals still count as armor, this causes the WMD damage to compartments to be multiplied beyond what it should be. While armor-penetrate weapons often should have reasonable WMD, the game should not add a silent buff in this way.
(This may also happen in unusual cases where a shieldbuster weapon hits a shield with very low points. I haven't been able to test if this causes increased armor damage from the "run-off")
Also: One thing that needs to be tested when this is fixed: If Armor penetrate works as a negative resistance, it should allow weapons to damage armor that they wouldn't otherwise be able to (eg. meteorsteel)...if the armor penetrate value is high enough.
Whatever fix is applied to WMD+AP *has* to allow for that to occur with compartments as well. IE: When the armor reaches 0hp and the internals take over, it doesn't suddenly become completely immune to the previously damaging rounds. Possibly take the higher of the two damage values or average them? (AP and WMD)
I've fixed this in 1.8 Alpha 1.
I compute two different values, derived from incoming damage:
1. How much damage the armor absorbs.
2. How many HP the armor loses.
For armor penetration damage, the armor takes more damage than it absorbs. For resistant armor, the armor takes less damage than it absorbs.
If armor reaches 0 hp, the original damage passes through, without AP modifier.
NOTE: Before this change, internal damage was being adjusted by armor resistance, even after armor reached 0 hp. After this, full damage is going to pass through to internals (though it will be modified by WMD).
We may need to increase internal HPs to compensate, but I think this is the right path.