I think the idea is if they do a wholesale swap out, all it takes it for anyone in the chain to look at it, realize it's fraudulent, and deny the return. If they use the correct sleeve with an errant disc, the UPS Store or Amazon worker needs to actually look at the disc. Much less likely to be caught. They also may scan them back in at some point (hypothetically) and an old busted sleeve may not have a barcode to use.
(Edit: I suspect the more common scenario is that someone has a beat up junker of a copy of Album X, buys a new version, and swaps out the junky one for the new on and returns it - damaged sleeve or disc or both - the full different record swap is riskier for sure - though I have had a couple that were just way off)