I haven't done it for a while..though I did ask when the program changed to on-line. I was told at the box office that if there is a choice, they will generally give the better seats to the lottery winners . The lottery seats are usually where the in person lottery seats used to be- which was primarily on the far sides of the orchestra.
The rush tickets are more random and can be anywhere in the house.
That said, these "rules" are more likely to be in effect on a day when it's sold out or close to sold out. If there are a lot of empty seats, you might get better seats no matter how you get the discount tickets.
Like all on-line lotteries, it seems harder to win than the in person lottery days - when the amount of people signing up daily were far less.