I understand how it works at the airport. I work in the travel industry.
Where Disney checks ID is when you check your bag at the RAC desk. They are required to do that because they are acting as agents of the airlines. They cannot accept bags without checking the ID of the owner, and comparing it to the boarding pass.
The reason it works on a cruise ship is that the cruise line is simply taking your bags to the pickup area. No TSA or other security. For checking bags at a Disney resort, you are checking them to be taken to your flight, put on the plane, and on to your home airport. Security must be complied with in that case.
This sounds as if it is something that has changed since your last trip, likely due to a need to comply with security protocol for checked bags.
EDITED TO ADD: I was curious, so I did a Google search for "Magical Express Departure Letters", and found images of letters as far back as 2015. None of them gave the option of leaving bags outside your door. All mentioned having to take them to the RAC desk and show ID. Could you possibly be misremembering? Or was it even before then? I didn't find anything earlier than that.
