The problem with this analysis is that it seems to analyze the subject with the assumption that the intelligent designer does not have bounded rationality. If we want to use articles like this to truly reject declarations of intelligent design of lifeforms, we must then attack intelligent design's declaration that the designer does not suffer from bounded rationality. Otherwise, it's constructing a strawman to take down intelligent design. The debate needs to be more rigorous, if there is to be a debate.
The point of the article was to show that Linux works differently then a real life form. E Coli being a product of evolution is already a settled issue, as far as biology is concerned.