The term 'prototype' can refer to a very wide range of hardware configurations.
An engineering prototype for the Pyra could consist of the SoC manufacturer's dev board connected to a display and a keyboard that is capable of running the intended OS.
Case design prototypes can consist of non-working unpopulated boards - or even stand-in pieces of cardstock assembled in 3D printed cases.
Early functional prototypes may have populated boards that do not function entirely but are able to test particular features. They may or may not even have cases - or the cases themselves may be 'incomplete' or require modification by hand to tweak for usability - and to understand what to communicate back to the component manufacturers.
I believe all of the above to 'exist'.
For the Pyra there is a group of people who have paid for prototypes. These are generally expected to be 'production minus one'. I.e. fully functional SoC boards connected to fully functional keymats held in fully functional cases. Essentially the final validation point for everything prior to ramping up the actual mass production. In a lot of threads on these forums, it is these final pre-production units that are often referred to as 'prototypes'. In reality, there have been many 'prototypes' made along the way through the process of designing, developing, testing, tweaking and finalizing the hardware.
From ED's messages, it sounds like this latest batch of cases is intended for use in generating some of the 'production minus one' generation of prototypes. Maybe it would be better to call them production beta-test prototypes?