Not sure that this is true. The flight timetable is normally based upon the average flight time between city pairs on teh company preferred route. Some days you will lose time as a result of a head-wind, on others gain it through a tail-wind. In most cases the aircraft will operate flight between a city-pair and then back again, winds typically averaging out
You are correct, it is based on that, plus a bit extra. I probably didn't state why I believe it takes place well enough in my post and to be fair it's usually not for commercial reasons (although perhaps the desire to stay on-time could be classed as that). The schedule has to take many factors into account (winds as you identify), plus contingency time. If padding didn't happen, there would be issues as the scheduling would be insufficient. The contingency time is the padding, which I feel is justified on any mode of transport.
Don't get confused by the timetable saying that the flight takes 1 hour 15 and the pilot saying that "today we have a flight time of 55 minutes". The "flight time" is time in the air, the timetable has also to allow for the time to push back off stand, taxi to the runway and taxi from the runway to the stand at the other end of the journey.
It's always gate-to-gate, I am aware of that. However, some airports will obviously have quicker taxi times than others.
------------------------------------------------------------------------------------------------
In any case, swerving back to the railways after this OT diversion, it is better to give a later figure of arrival (and then arrive before that time), so passengers can book rail tickets at an appropriate time. Encouraging rail use to/from the airport should be a priority, it does seem to be an after thought at some provincial airports. Teeside Airport being the prime example of an underused rail facility. I know it isn't directly near the terminal, but it does seem like a lost opportunity for public transport journeys.