[HEIS]

Claiming the goods were missing from the box/package Is obviously not a theft-related Incident, hence a PR Is not warranted.

Tell Amazon to justify their request.

been there done that
I bet that their justification will be pretty much copy/paste the same PR request email over and over again. They don't feel like justyfing is needed, since they suspect there was a  criminal activity they'll just keep being stubborn about it (even if it's amazon who will be named as the probable fraudulent shop in the PR, they're ok with that). 
And imho it's not a stupidity stubborness but more like procedure, anti fraud stubborness which might look absurdly (especially for legit cases).
Any discussion or escalation attempts will probably either end up with a loop of the pr request or just silenece. I wish you good luck though but I feel that PR will be necessary.