Are cargo and passenger flights flown differently?
Yes, cargo and passenger aircraft of the same basic model are sometimes flown differently when there is no live cargo. A friend of mine who flies cargo put it almost exactly as you did in your question when you say boxes cannot complain, so he sometimes hand flies the aircraft when passenger pilots would be required to use autopilot. Cargo pilots don't have to worry about tender stomachs in the back, so steeper climbs and descents and tighter turns are acceptable as long as the aircraft remains well within the flight envelope.