Still not how it's done. When I switched out my 6S for the 6S Plus, I didn't have the charger or the cord. Still got my iPhone exchanged without those items. Apple didn't take them out of the 6S Plus either. If he exchanges the phone alone, they replace everything irregardless of whether he or she brings in everything for the exchange. The accessories included are minor. If the OP had to mail it off, then they only ask for those accessories. But the phone in a clear plastic case, does set off alarm bells. Why? The box that the phone comes in, (the original box) has all the pertinent information just in case you can't access the phone. If this "clear" box has that info, then I rest my case. Otherwise, this is how it's done.
Warranty and out of warranty replacements have always been the device itself, and only the device. Even when you send in a device for Express Service, the instructions for packaging the damaged device will clearly state to not include any cables or accessories as those are not part of the warranty exchange.
A return or exchange during the 14 day unconditional return period, or a trade up exchange, are different.