As I was unaware of the short course body rule until Saturday morning when this issue blew up I can't say too much other than my opinion on this. While I agree the body should have its scale appearance I don't think the twonie size holes should be allowed either. I think after looking at the real thing and seeing many real trucks are open completely in some cases on the bed cover with only roll bars being visible and some appear to have a cover with vents for aerodynamics. Body parts come off of them often with only sponsors of lost parts being upset. To me what looks scale are cut along body line without any circular holes unless it is a molded cut line. In the case of the large open rear my personal feeling is open all of it up leaving just the roll bars or leave it. If structure is a problem then reinforce the area and or add a mesh screen to maintain scale appearances.
Keep in mind these are only my suggestions and opinions as I had no part in the body rule.