Interesting article. I have been running a road/race series here in NZ for 16 years for European cars. It is unique in NZ in that only the handicaps count for points. The format for each race meeting is one practice, 1 scratch race (no points) and two handicap races.
I develeloped a straightforward spreadsheet programme that records all fastest laps in each practice and each race and without getting too deep, it takes into account the first lap (being slow of course) and that difference varies from track to track, so there are spreadsheets for each track.
As weather conditions can make a huge difference to lap times, there is a column that has a weighting between past history and the current weekend. That means that if wet, it might be 4 of today's best, added to the best historical lap, divided by 5. When it is dry and 'normal', then the weighting is changed to 2:3 or 3:2.
We generally get the whole field of 25 to 30 cars through in less than 30 seconds, BUT, if the result is poor, it can be from several factors, not limited to a yellow flag, unintentional blocking or in rare cases, a row not going off the line when it should.
We "interfere" with the system so as to penalise any driver who maybe had an unfair advantage previously or may even have already won a race or two, as the aim is as you say, to get every car across the line at the same time and for the series to retain interest and annually, to get a different winner each season. It must work as we have two grids at each meeting!