If the application is a window into your data, why make that window bigger than necessary, thus obscuring your desktop, or some other window behind it? That may not be disastrous, but I think its intent makes sense.
Without further explanation, I end up suspecting that when he writes: "it almost never does what you’d want or expect it to," the emphasis is on his expectations as a Windows user, not on what he would prefer, all things being equal.
[and for the record, I'm speaking as an Ubuntu user, who has never owned a mac]