The one like Shadow of the beast are Atari Original protos.

 

Do you mind sharing how you can be so sure? Between Best Electronics, Video 61 and B&C all having access to original Atari prototype parts and frankly all three of them having no concerns about building their own protos and selling them, I can't see how anyone can be sure. Similarly, that seller on Ebay, Misfit Toys had a lot of Video 61 stuff mixed in with his other items, so it's clear he at least bought some items from them and perhaps other vendors. He also never really explained what he did in the 15 years he claimed he worked at Atari. In any event, unless you find something that comes directly from the programmer or someone else that can establish a chain of custody back to Atari, I would be very skeptical of any Lynx protos out there.

Source: Worth of "released" protos