"Invalid", "CapitalAbility", and "PlanetBombardment" are the only you won't use for ship/def/starbase weapons. Probably a lot here you already know.
In the weapon research, there is the researchfloatmodifier group and you can have up to 6 researchModifiers.
baseValue -especially useful with WeaponIgnoresShieldsAdjustment. Setting to 0.300000 gives 30% base shield ignore to the linkedWeaponClass. Not so good with others unless you just want beefier stats right off the bat without getting into changing the ship/def/starbase entity file and all that.
perLevelValue 0.000000 : 0.050000 is 5%, 0.10 is 10% bonus, 1.0 is 100%, 2.0 is 200%, etc...
linkedWeaponClass -AUTOCANNON, BEAM, CHAOSBOLT, DART, FLASHBEAM, GAUSS, ION, LASERPSI, LASERTECH, MISSILE, PHASEMISSILE, PLASMA, PULSEGUN, SPIRITBLADE, WAVE.
Any weapon can be given WeaponIgnoresShieldsAdjustment. Autocannons, plasma, ion, etc... Just put weaponignoresshieldsadjustment in modifierType and then any of the above into linkedweaponclass. Bingo, AC's and plasma can pierce shields and pass x% of damage to armor.
I don't deal with Diplomacy, but Entrenchment. In Diplomacy, you might be able to add this (from shield pact unlock) into high tier shield research item to negate any weapon that has WeaponIgnoreShieldsAdjustment regardless of linkedWeaponClass.
You can always modify the player entity file and give them the pact stuff for the shieldignore block.
I wonder if it'd work with entrenchment? NO, "ChanceToIgnoreShieldsAsDamageTarget" doesn't. It only works in "BuffAdaptiveShields.entity" or other buffs like it. We gave empire a shield research that unlocks an ability like AdaptiveShields that give 100% bonus vs any weapon with shield ignore properties because Empire has armor that sucks -a single fighter can destroy one on a kamikaze run into the bridge. Ability is in the ability4 slot and out of the way.