I might actually have an answer this time instead of me whining about not having the answers; unless of course I've misunderstood your question.
Are you just wanting to face the top surface of your stock to z=0 or do you want to surface the top and sides of your stock all in one operation?
I wasn't able to use the Roughing-Plane Operation to do both. I had to use the Roughing-plan/surfacing operation just for the top of my stock and then switch to the 2D section and do the sides.
I think this is a situation where there's the "Right Way" to do this and then there's the way I've muddled together in order to achieve the same outcome. I'm flying by the seat of my pant and hope I don't crash.
In either case I think you still have to go into SprutCAM's Stock Perimeters and add some stock to your work piece first; at least that's how I managed to get results.
I hope I'm using the correct terminology. If I've just added more confusion just disregard this reply.