"If these anomalies are seen by the breeder, and then the said animals (and parents) are not allowed to breed or culled completley for humane reasons. Wouldnt this be the same as natural selection or are the variables of nature much more complex?"

No, and yes. When animals are bred to first degree relatives (f.i. brother to sister), each generation they loose 25% of their genetic variability on average. Visible anomalities are easy targets for selection, but it's the loss of genetic variability and thereby the accumulation of countless minor genetic defects which in the end will cause the demise of any linebred bloodline. Some will be sooner, some will be later, but the outcome is inevitable.
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