This is a good example of hacker writing in 10 paragraphs the sort of thing that has often been diluted into a 250-page business book.
The missing piece is how to identify over-specialization, and it's missing because it can't be usefully generalized.
If you read the literature on selective breeding they have extensive methodologies for avoiding genetic problems. If you just want a quick overview, Temple Grandin's book "Animals in Translation" has a couple of really entertaining chapters on the subject.
We've been using biological metaphors in this discussion, but I'm not sure we can extend them this far.