The selective breeding and the implant are different thing. With the selective breeding they take an species closer to the extincted creature and start to breed them with other similar species until they get an individual that is closer to the animal they are trying to "recreate". It is not cloning, but it is also as good as they can get given that they did it to some species already (they are never going to be genetically the same as the extincted species, but neither would cloning)
Although the problem you pointed out is real for this procedure too.
Carter Roberts
How can you forget Polly? She was the McGuffin of the whole movie too!
