Shooters, Registered Mag's, inherited guns, prized possessions or whatever......... none of us like rust! Every gun distributor, gun store and wholesaler stores the guns in their original boxes until they are sold.
What is MORE IMPORTANT is the surrounding environment. If you have a damp basement, garage, or room in which your safe is, I don't think storing a gun in its original box, gun sock, gun rug or just on a shelf is going to make a big difference. The MOST IMPORTANT thing here is to make sure that the surrounding environment is not humid or damp. If your gun storage room is clean, dry, heated in the winter and a/c cooled in the summer you should be just fine regardless of the storage method and assuming a light coat of oil is applied prior to storage. If you have your safe in a damp basement or garage - weather the guns are in the VOC paper in their original boxes or in a gun rug, sock etc. isn't really going to determine rust or no rust, it's the surrounding environment!
If your safe MUST be kept in a non heated or air conditioned environment, than I would suggest getting and using a Golden Rod or some sort of dehumidification system in the safe. If you live in a very humid & damp climate you might want to consider RIG UNIVERSAL GREASE being applied to the gun and wrapped up in wax paper. Rig Universal is (as far as I am concerned) the absolute BEST in preventing rust long term for infrequently used guns. The best solution is just to keep the safe in a steady cool & dry location - then exactly how you store the guns and in what container, box, rug etc. is really a moot point IMHO.