The camera is made by Cosina under contract for Carl Zeiss AG. While Cosina had some input on design and materials, it is not a Bessa clone. Carl Zeiss had the final say on the camera.
The physical dimensions of the camera are markedly different.
The Zeiss Ikon, from what I understand, is produced on a separate line from the Bessa. And each body undergoes testing to meet Zeiss quality control standards.
I haven't handled any of the recent Bessa cameras, but in general the bodies have improved with each successive model.
The Zeiss Ikon is a German camera that is made in Japan. That might be a good way to describe it.
The Zeiss Ikon has a very wide base rangefinder and large viewfinder. The camera has varnished magnesium for the top and bottom plate. The camera doesn't use foam to block light -- the back uses a proper labyrinth design.
All markings are engraved and filled, rather than painted on. The Copal electronic shutter has been modified to meet Zeiss demands. If I recall, the modifications were aimed at decreasing the shutter noise.
Because of the width of the rangefinder and the location of the viewfinder on the extreme left side of the camera, the rewind knob has been moved to the base of the camera.
The camera back can only be released by pushing the slightly recessed button in an "L"-shaped pattern. It's very effective, and accidental opening of the back is nearly impossible.
As I mentioned, I haven't handled any of the recent Bessas. But the sense I got from the Bessa-R and the Zeiss Ikon is that the Zeiss Ikon is a more refined camera with better choice of materials, a more accurate rangefinder, autoselection of viewfinder framelines and overall excellent operation.
The Bessas are good cameras. The Zeiss Ikon sits in a nice market spot by catering to those who want more than a Bessa but can't afford a Leica.