You’re lucky to have the R3 box… They are something of a rarity, and frankly a better setup than the R2 sealed carb with ‘bonnet’ on top of the carb factory setup……..
Yes, Studebaker shimmed up the fiberglass Avanti body off the frame, similar to what the Avanti ll folks did… Studebaker did that for air box clearance… They also removed the horizontal underside hood brace and used thinner ‘R3’ type front engine mounts… Good luck with your interesting Avanti!…. Ed