I have a scene that requires one object to glow. I placed that object on it’s own render layer and enabled transparent under the film options. I set up the composite and everything works, except I have no sky (Using Pro Lighting Skies). So my current work around is to take my blend file and save a second one. One of this is for the main scene and has the transparent switch turned off, the other is just the object and has transparent turned on. Send them to the farm and composite after in either Blender or other third party.
My question, is there a way to have the transparent option only affect certain render layers, rather than the entire project?