Yes, it makes a difference. Taking an overnight flight from the West Coast through for example Miami/Charlotte will put you into to SDQ pretty much at the height of arrivals: busy time. So going overnight from the West Coast does not avoid the "2 hour wait in line". The only way around it we have ever found somewhat, is taking a day flight to the East Coast (NYC, Philadelphia, Newark) and then waiting around for the middle of the night flight. There are flights from NY that leave late at night or after midnight which would get to SDQ somewhat before the "rush". But that is a long day compared to 4 hrs. (approx) to Miami/Charlotte then 1.5 - 2 hrs. to SDQ. For many avoiding the "2 hr. wait" is not possible given where you are coming from. That is why some choose to use the Before Boarding option. Sorry but when I fly those flights I want to land and get out of the airport as quick as I can. Worth the price.