Does it really take 2 hours to clear quarantine inspection during peak times? I've never had it take more than 15 minutes (seems more like 5 is the norm), so do such long delays happen routinely? Also I'm not quite sure what "daily midnight departures" have to do with arrivals delays.
The advice for all passengers to check-in luggage 3 hours prior to departure, even for domestic flights, is a bit suspect. Doesn't check-in open about then -- I've heard of baggage check-in refused more than 4 hours prior to flight time. QF domestic baggage check-in is still 30 min at MEL which is a bit different from 180 min.