Yea Wind Waker’s the only game I’ve seen to do such a thing with it’s alpha. Though from what I can tell, they seem to have some system where you can scale the alpha of an entire particle emitter uniformally, rather than having the particles scale individually. All of the particles in the core smoke of the explosion fade alpha at the same time, so I doubt the effect would work correctly if they had staggered lifetimes.
Meanwhile other effects in Wind Waker, such as the debris trails from the explosion seem to have far more typical alpha sorting.
You can see here the debris trails overlapping as their alpha fades.