Oh, I see what you mean. Good question. I suppose it might have been more efficient to avoid multiple colour buffer overdraws (since you're drawing a fullscreen quad for each seed point, albeit a depth-tested one). And you could render the depth+stencil buffer once then reuse it to highlight different regions, e.g. on mouseover.

But you're right, it doesn't sound massively compelling. And the traditional 24depth+8stencil buffer format would limit you to a maximum of 256 regions, which could easily cramp your style.