I think there needs to be a guide to cover this since it’s been a source of much confusion since the release of Ashes of Malmouth, and in some cases even before that. This is a short reference sheet and FAQ on this obscure game mechanic.
Secondary skill modifiers is, as the name suggests, a special kind of skill modifiers – basically a node in your skill selection screen. In-game they are absolutely indistinguishable from normal skill modifiers and you won’t find any mentions of them - the name “secondary skill modifier” is an internal term used in mod tools.
The quirk of secondary skill modifiers is that other skill modifiers do NOT apply to them, even though they seemingly should and the game straight up suggests it in some cases. Some things like %damage skill modifiers are neither noticeable unless you dig deep, nor they are terribly important. Conversion skill modifiers unfortunately are – this includes both transmuters and item skill modifiers.
The exception (kind of) is a buff-type secondary skill modifier. These apply a buff to player if a skill in question lands. If there’s a conversion skill modifier for the skill in question then it would NOT convert the flat damage on the buff it applies in a global manner, BUT the applied buff is global, so if you re-use a skill (while the buff didn’t expire) it would properly apply it’s conversions (if applicable) to the damage from it’s own buff (provided skill got %weapon damage component).
Secondary skill modifiers are boosted by global bonuses.
The rule of thumb for dealing with skill modifiers is to consider them an extra devotion proc. If something should apply to a devotion proc bound to a skill then it would also apply to the secondary skill modifier. I don’t know any exceptions.
List of Secondary Skill Modifiers
Deadly Momentum (buff type)
Lethal Assault (buff type)
Soul Harvest (buff type)
Heart of Wrath
There are two kinds of fragmentation - native and added via modifiers.
Native fragmentation is a basic property of a skill, meaning that skill has fragments by default. Example of such skill is Canister Bomb.
Fragmentation added via skill modifiers is exactly what’s written on the tin, examples are Brimstone, Vile Eruption and Proliferation.
The mechanical difference between them is native fragments receive full flat bonuses of other skill modifiers, while added fragments do not. This includes item skill modifiers. Conversions applied via skill modifiers also do not effect projectiles that were added via skill modifiers.
A super amazing example here is Panetti’s Replicating Missile that has both types. The fragmentation from Panetti itself is a native fragmentation so it receives damage bonuses from Distortion and Supercharged and will be converted by skill modifier conversions. Proliferation on the other hand is the added via modifier type, and projectiles spawned via Proliferation do not carry damage bonuses from Panetti itself, Distortion or Supercharged, neither they receive any bonus or get converted by skill modifiers.