As I understand it, Koryu Uchinadi is the name of a group headed by Patrick McCarthy and although contains the word "Koryu" in the title is most definitely not a Koryu (and I know you are not saying that it is).
To be fair, if you read the blerb on his web site he says as much, and perhaps uses the term "koryu" in the sense that it is "old school methods" - from a perspective of karate in order to re-connect with the origins of the art.
Although I am a member of a Koryu group, my experience is limited - so my words should be read as that of a novice, however I do feel that the key is in the word "Koryu" and understanding what that means.
I have read with pleasure some of Chris' posts on this board and concur that it is more about the continuity of the Ryu - the stream as it were and I think that's the difference.
As far as I can see, koryu Uchinadi is about the re-discovery of ancient ways and putting them back into practice (which is great I hasten to add). In Japanese Koryu, the ancient ways have been continuously practiced, therefore never lost and further more built upon for generations - a very organic process, in that is a stream of consciousness that has continued to flow for generations from teacher to student.
Think I have confused myself with that answer, but then again as I said Japanese Koryu is a very new and scary thing for me.