The tone of the whole thing is fairly flippant, really (an experiment with a different style of writing which I haven't used since!). I certainly wouldn't criticize anyone for using a standard tuning, indeed I do so myself most of the time. Like I said for one thing it makes collaboration (with other musicians or instrument-makers) easier, then there's the fact that the standard tunings themselves form part of the cultural background we're building on when we make more music. For example if we take the roughness plot in the article as representative (which vnorilo rightly calls into question, but still) we see that any interval in the continuous range between an 5th and octave is evaluated as smoother than a minor third. But we don't perceive it that way, I suspect because of our cultural background.

If you want to make an apple pie you must first invent the universe.