Wonder if I have to test all the different damage taken modifiers as well (for example, how Graviton Beam stacks with Entropy Amplifier, etc.).
I think pretty much all damage taken modifiers are multiplicative with everything. Even the ones that modify the same mutable stat (graviton and amplifier, for example), modify the multiplier of that stat, rather than the flat or the percentage.
Here's a list based on code digging, as opposed to testing:
Group A (everything inside is additive, the group itself is multiplicative with others):
CR (assuming CR > 70%)
Ballistic Mastery (regular and elite)
Tactical Drills
Energy Weapon Mastery
Cybernetic Augmentation
High Energy Focus
High Scatter Amplifier (regular and s-mod)
Missile Specialization (elite)
Group B (everything inside is additive, the group itself is multiplicative with others):
Target Analysis (regular and elite, part that scales with target size)
Wolfpack Tactics
Advanced Turret Gyros (s-mod)
Point Defense
IPDAI
Defensive Targeting Array
Terminator Core (hullmod on Tempest drones)
Special ones (multiplicative with each other and everything else):
Targeting Feed
Target Analysis (bonus damage to engines/weapons part, technically a flat bonus, but it's the only one in its group in vanilla)
Damage taken modifiers are all multiplicative with each other and everything else:
Graviton beam effect
Entropy Amplifier, Damper Field, Fortress Shield, etc
Impact Mitigation, Damage Control, Field Modulation
Resistant Flux Conducts, any other hullmod that modifies damage taken
Bonus damage from weapon listeners (Squall, Breach, etc). Despite being worded similarly, these are implemented dramatically different from one another and scale differently with multipliers above.
An interesing subgroup is Mining Blaster, Breach SRM, and Disintegrator. Bonus armor damage of these is implemented similarly: they scale with bonuses that are based on target size (group B from above), and damage taken modifiers that affect armor damage (Damper Field, Amplifier, etc). Everything else has no effect on their bonus damage part.