There's currently no fight in the game (aside from the first boss of Neverreap) where adds/jumps happen before you finish your opener. I still haven't optimized that terrible, terrible boss fight, because it's too full of RNG to make a proper rotation out of it.

You should always get through your second Heavy Thrust before you lose targeting on the boss and/or need to deal with adds. The only other one who does different is Fractal's final boss, where the adds spawn just as you hit True Thrust (allowing you to SSD to the adds to kick their butts and gsk a few of them before going back to the boss).

So, yes. You should be using the base rotation always. In every single-target boss fight. In the current meta, there's very, very little that mucks with it and forces you to do anything other than stand there and poke the boss like it's a training dummy. The hardest encounter in the game right now is a series of 5 dummy fights back to back with a few adds to kill here and there (as a melee dps).

Any single-target encounter that matters should let you get through your full first botd timer without interruptions, at the very least. If you're struggling with maintaining this, you need to evaluate what the boss is doing and adjust your playstyle (not the rotation) to accommodate the different things the boss does. I unfortunately see a LOT of melee dps dodge aoe by running AWAY from the boss. This is bad. If you're doing this, ever, your group is either using poor strategies or you're purposely making your rotation harder to maintain.