It sounds like this is a common approach. Is this why there are subtle difference traits in lines among a breed? I was under the impression that grading was frowned upon. For instance the Garfield Farm in Illinois did genetic testing on their Java’s to prove they are a genetically unique breed. I’m not taking sides I’m just curious.
These are good, well informed questions. I'm not sure there is a simple, concise answer, but I will share my thoughts.
Differences between breeders lines will happen regardless of whether foreign blood is introduced. Many reasons for this, foreign blood can be a factor at times, but I'd suggest more often than not the differences lie more in personal, selective interpretation of the Standard, and personal biases in regards to breeding choices .
Regarding Javas, I would suggest this is not the best comparison. The Java is one of the old foundation breeds, the Cubalaya in comparison is a fairly modern composite breed. We have rather a good idea of what went into the Cubalaya, the Javas origin is lost in the mists of time. Javas were at one time common practical farm fowl in general use, kept and bred by many people in large numbers, and hence the genetic base was large. Cubalayas have never been bred in the United States in large numbers, were essentially always maintained as Exhibition fowl, and descended from relatively few imports. In my experience the breeds and breeders that boast of closed flocks for decades, no new blood for decades, primarily are breeders of the American Class fowl that were bred in huge numbers historically , that were heavily selected to perform as practical livestock. These breeds seem to have what it takes to function reasonably well without new blood for long periods of time. Many if not all of the rarer breeds and varieties have had fairly frequent infusions of outside blood out of necessity. Generally when seeking a breed to cross to, the least number of problems to breed out, the better. You want something quite similar or as similar as practical.