Another case that would make a difference on DL is direct flights. If a single flight number does AAA-BBB-CCC, all domestic, someone ticketed to fly from AAA to CCC on this "flight" (which is likely to have a change of aircraft and even aircraft type at BBB) can only be upgraded if both AAA-BBB and BBB-CCC have upgrade inventory simultaneously, so that folks flying only AAA-BBB or only BBB-CCC on this flight number would have an advantage. This is regardless of other connections that these passengers might have.