Applying stopping compound on plywood
Yes, you can skim coat the plywood.  Use an oil based primer first, then instead of topping compound use setting type compound aka "hot mud", the type of compound that uses plaster of paris.  This type of mud is stronger and adheres better than premixed topping compound.  You will mix it a bit watery, like thick paint, and can put it on with a roller, then use a squeegee to level it off.  I did this over wooden paneling, and it worked pretty well.  It will probably take a couple of coats to level out everything, especially at the joints.