The BBC, not having specific advert slots within their schedule (but feeling the need to promote their own output), occasionally start and end some shows a few minutes before or after the indicated times on the EPG. For many decades BBC1 has had scheduled weeknight shows which nominally start at 7pm but have actually began at 6:58 or 6:59pm. This latest run of TG has indeed overun the nominal 9pm finish by a couple of minutes.
It is not true that the EPG timer starts and finishes with the programme otherwise there would be no need for the ability to offset the start/end time. I have mine set for 2 mins either side which has yet (so far) to fail me.