The teams did not take into consideration that it was the distance travelled (McLaren was further back in the staring grid) when they went for the 'photo op' of all three crossing together. Thus the black GT of McLaren's didn't have to cross the line first to have travelled farther. I believe you are just mis-understanding the explanation.
I believe the 'distance' theme was already in the 'rule book', though that shouldn't take away from the understanding that the French would make up rules as they went along. Colin Chapman refused to return after a particularly difficult scrutineering one year.
BTW - the 'Heritage or Gulf' colors refer to the final 2 wins of the Ford GT40 while under John Wyer Team management and Gulf Oil sponsorship. 'Heritage' does not refer to the Mark II's.
I have always been entrigged by the Ford Racing History in the 60's from the Cobra's, GT40's to the Mustangs etc..
This site from the UK seems really comprehensive on the GT40 Lemans History. It lists all cars and numbers and drivers from 1964-1969, very detailed information.
http://www.gt40.org.uk/Le Mans/index.html
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