Hard to know what is included in the Intel reference design (since the general public can’t see it). It probably does include an example laptop enclosure because Intel wants the laptop manufacturers to get the thermals right. I know that Intel promotes a standardized keyboard, so I assume that is also included in the reference design.
However, I would assume that the ODM used by Purism has its own laptop case design and Purism asks the ODM to modify it to add kill switches, so the ODM is the copyright holder and not Intel.