A record is not a record until it has been certified by the FAI (Fédération Aéronautique Internationale). They require that a record attempt should be notified in advance and that the time is measured from over the top of the departure tower to over the top of the destination tower. The tower operators log the times and advise the FAI. The FAI website is
www.fai.org/records. If you are interested to view their records for airliners (Class B) go to record I.D. 1766 which should show the fastest sector time in history as certified by the FAI. (1132 Km/hr from memory. Perth to Melbourne) If the entry is still green then it is still current for that sector. Just for interest, for that particular attempt, the cowboy irrresponsible crossed Perth tower in his B727-100 at 350 Kias, cruised at M.87, and again crossed Tullamarine tower at 350Kias at 2000 ft! 2 hrs 11 mins I think.