I troubled through something similar last year. This is not an issue w/ the Toon Render.
I have a method that works, although not as simple as it could be for PNG. It seems that what is needed in the PNG Buffer Options is the Shadow toggle (present in Targa).
1. Set the file type to targa
2. Set Buffers
a. Alpha = on
b. Shadow = on
3. Return file type to PNG
4. Render. You know have a layer with the shadow (and the toonlines)
5. Go back to targa and turn off buffer:shadow
6. Return to PNG and render to a new file name. This will be the object.
Hope that helps.
Click to view attachment Click to view attachment--Tim