Where do you get the "high 90s" punctuality from? I am not aware of any airline that can claim this.
According to
this, BMI, who are the best performers on the Edinburgh-London route, achieve a punctuality of 76.57%. This is defined as arriving within 15 minutes of schedule. The average amongst all airlines for that route is even worse at 67%.
In other words, one in three planes takes more than 15mins longer than the scheduled time, ie. more than 1hr 45, presumably
By the way, as far as I know, punctuality on the East Coast Main Line from Edinburgh to London is now at about 90%. That is defined as arriving within 10 minutes of schedule.