My Bodyguard 380 came in a cardboard box - but my M&P 45 has a plastic case and a buddy's recent M&P 22 also has plastic case.

I believe the instructions from most manufacturers on return indicate that you should NOT include any thing but the firearm and possible a single magazine (although that may depend on if the issue may be related to the magazine).

It would be nice if a shop would as a courtesy to the customer keep track of everything that arrived in an RMA package and keep it all together to make sure it is all returned. Not sure about damaged or broken parts that are replaced, but whenever I have had automotive work done there was generally a check box on the estimate indicating that you wanted any removed parts returned to you. Of course in the automotive world broken parts often have a core value or at least scrap value.