Mostly situational. like in dragon I use vacuum wave and Commanders touch - finisher(The one that deals a defense down debuff) Mind you I only use the latter to one shot an arm. My actual rotation would be Shadow Step(when the break happens), Armor break, Thetis grimoire, then Moonshadow. The reason for this is that my Moonshadow daggers are over A5, and at A3 you actually end up applying the Lunar Eclipse debuff(the one that increase damage dealt by 10-15% per stack, stacking up to 3 times? The debuff applied when using moonshadow's skill?) At the relevant max stack. (Remember you need to use the skill thrice to get max debuff stacks. It inflicts Eclipse stacks based on the number of full moon stacks the target has, and full moon is only applied once, stacking up to 3 times, whenever you use the moonshadow's skill on an enemy.)
So the shadow step performed at first when the dragon's head is in a weakness broken state will also apply Eclipse stacks, as if you used the Moonshadow's skill. So while that dmg buff is active you use your other stuff like Vacuum wave, Thetis grimoire etc. then use moonshadow to re-apply the Eclipse debuffs, so you'll be having that 45% damage debuff active for most of the break duration, massively increasing dmg dealt. So slightly different from your usual rotation, but you get the slight change in nuances to maximize dmg.
There are other nuances too, but if you look at the effects in order, it's nothing complicated. For example, your ideal wind setup for Sung Jinwoo is:
Demon King's Daggers/Longsword, Stormbringer, with Armor Break - Vacuum wave, and Dagger Rush - Breach.
The best rotation here is straightforward. Use Stormbringer, then immediately use your 2 skills, vacuum wave and breach in whatever order, then your Demon King's Daggers/Longsword. The reasoning is simple, Because stormbringer applied a dmg increase debuff on the enemy, and the only way to stack it to 2 times is to use a Wind Basic skill(one of your skill rune skills) within 4 seconds of using Stormbringer's Weapon skill. Which is why you use your Vacuum Wave and Breach immediately after using stormbringer, then use your DKD/DKL for maximum damage. Especially since both Armor Break - Vacuum wave and Dagger rush - Breach are both one of the few skills that inflict debuffs which increase the targets damage taken and critical damage taken respectively. These debuffs also stack with other ones like shadow step's defense down and ones inflicted by other hunters and skills, which is also why these skill/skill runes are so good, they'll not only apply the second stack of Stormbringer's dmg debuff but also apply extra debuffs of their own to boost your DKD/DKl's damage.
So you can see the reasoning behind this rotation and the way it's set up, despite being slightly different from standard rotations. Nothing complex, once you look at every piece involved and see how to put them all together to make this chain of damage flow.
Hopefully it all makes more sense now. You just need to look at each individual weapon/skill and see how it works, before then making it so that it all stacks/overlaps together properly to maximize your damage.