My guess is because airdate order is the standard for DVD season sets (at least in the US) and since that's the way the series was originally run, etc. blah yadda. Of course, there are exceptions (Firefly and so on), but in the long run, how much does it matter? Do the majority of people actually sit down and watch the series from beginning to end, or do they pick and choose episodes? This is the first time I can remember watching them in this order intentionally.
For stardate order, let's travel back to the glorious days of the Columbia House releases where they actually put them in that awful order. You think airdate order makes no sense?