I noticed an old thread where someone posted about phase missiles not working correctly (specifically in conjunction with Advent phase missile blocking in culture upgrades), to which a dev replied stating it had been fixed. Whilst working on my mod I noticed that it seems to be broken again (or perhaps it was never fixed?).
For my tests, I used an AR and a VR faction. I created custom research to adjust the values of ChanceToIgnoreShieldsAsDamageTarget and CultureChanceToIgnoreShieldsAsDamageTarget (the latter being the one used in the Advent culture upgrades), and also of WeaponIgnoresShieldsAdjustment, which the Vasari phase missile upgrades use.
I then used an AR capital ship against a fleet of VR long range frigates with various combinations of the research.
ChanceToIgnoreShieldsAsDamageTarget seems to work and display correctly. It takes a negative value to block missiles, and appears green on the tooltip. Setting it to a -100000% led to all damage being applied to the shields first. Setting it to 100000% led to all missiles bypassing the shields, again as expected.
CultureChanceToIgnoreShieldsAsDamageTarget (the one that's important as it's used in Advent's research) behaved strangely...
Like ChanceToIgnoreShieldsAsDamageTarget, it has a negative value to increase the block chance, yet it appears red in the tooltip, suggesting it's a bad thing.
At -100000% in friendly culture I expected all missiles to be blocked, since it's taking the default value to the extreme, however the missiles still bypassed the shields a reasonable amount, and the Advent ship was destroyed with ~800 shields remaining.
At +100000% in friendly culture the expected happened - all missiles ignored the shields and the Advent ship was destroyed very quickly.
Then I staged the battle in neutral territory:
At -100000% the research should have no effect since the battle is not taking place in friendly culture, so the ship should die more quickly than it did in friendly culture, but it didn't.
At +100000% there should also be no effect in neutral culture, but again all missiles ignored the shields just as in friendly culture.
Only a positive value for CultureChanceToIgnoreShieldsAsDamageTarget blocked the correct amount of missiles (i.e. none), but it did so regardless of friendly culture.
A negative value seemed to have no effect.
To verify this I raised the phase missiles' chance to ignore shields to 100%. In both friendly and neutral culture shields were 100% ignored regardless of how much I increased CultureChanceToIgnoreShieldsAsDamageTarget.
Conversely, setting the phase missiles' chance to ignore shields to 90%, and then setting CultureChanceToIgnoreShieldsAsDamageTarget to 10% led to the missiles totally ignoring shields again, in both friendly and neutral culture.
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TLDR;
The Advent research that is supposed to help block phase missiles in friendly culture doesn't work (no effect whatsoever, even after massively inflating the values). With a positive value instead of a negative one (i.e. making shields worse at blocking phase missiles) it works, but irrespective of culture.
So two issues, negative values of CultureChanceToIgnoreShieldsAsDamageTarget don't do anything, and all values of it are unaffected by culture.