The spec may not mandate that Accept and Content-Type match, but it's still pretty strange. The client is saying "I accept this particular vendor-defined format, with an underlying structure of JSON" and the server says "ok here's a blob of JSON". Nothing in the server's response indicates that the response actually belongs to the specific vendor-defined media type, it could be handing back arbitrary JSON.

I get that from a practical standpoint the server needs to send back a JSON Content-Type, otherwise a lot of clients won't understand that it's JSON and won't decode it properly. But given this, shouldn't they have picked a different header to declare the API version?

What's the benefit of using the Accept header in this fashion? AFAICT there is no benefit at all over just using a custom header.