Faking shadow of clouds on ground and geometry

I'm trying to fake the shadow of moving clouds on the ground and geometry in the most effective way. The cookie is a pretty good way to go, but the light is actually adding (as it is a light) but instead I would rather have a controllable element that could perform a darken functionality (or possibly multiply).

Another solution I thought of was the projector, and I've tried this. Yet this doesn't work on object's with transparent shaders as it can't skip projecting on the transparent parts. Let's say I cut a leaf out of a plane with a texture with alpha, the projector will still project on the full plane. So far I haven't found any decent shader solution for this work around it.

I was wondering if any workarounds exist for something like this? A game that succesfully does a good looking shadow of clouds is DOTA 2.