Sometimes hard to get the bean straw back to the chopper without all the plates in. Then it drops on the chaffer, and goes out unchopped. For what few beans you might save having the grate open, I'd put the plates in.
If you take them out for soybeans I will guarentee one thing. You will be climbing in the back to unchoke the shoe. Soybean stems will get caught vertical between the grate and the fingers in the chaffer preventing material from flowing out of the combine. leave them in and you'll never see this.