Of course, it depends on the effect, but…
For effects that create an overlay (like lightning) it is typically “better” to have the effect on its own layer (in my opinion) rather than “compositing on original” because it gives more control over the effect (blending modes, opacity, scale, position, etc.) and because if you change the affected layer for any reason, you don’t have to re-do the effect. Just a general flexibility thing.
I’m sure others have other reasons.