I think you have to remember that at the start of *every* breed of bird, there is outcrossing to other birds that don't share all desirable traits. It's not about what undesirable traits are tossed in to the first group of generations - it's about how well the breeder selectively eliminates the unwanted traits and keeps the improvements. Do you think no farmer in Indonesia ever cross a Cemani with another breed to improve a trait, and bred back? Of course they did, and I bet they did so often, before we ever heard of their breed of chickens.
Think about it another way. If a breeder bred Cemani but picked the lighter-skinned ones... or with redder combs... for generations, until they had a bird that didn't look like a Cemani at all - but never once used a different breed. Would you call that a Cemani, since it's 'pure-blooded'? Versus a breeder who cross breeds for a higher egg count and then breeds back to Cemani until it walks and talks like a Cemani (with a better laying count)... That's just one example.
I guess what I'm saying is - people need to relax about diehard-purebloodism. You shouldn't care what it was crossed with in it's past as long as the 'finished product' breeds true to the standard (or original tradition, in yet-unstandardized breeds like the Cemani).