Do not count QB kneel down at the end of the game or half as negative rushing yards
When a QB takes a knee to end the half or game it should not count as negative rushing yards. At this point the teams have decided the game or half is over. The defense has conceded. The offense has stopped pushing for more. This should not be a deciding factor in any games and cheapens the competition.
If you change your league's settings to give 1/2 point for each rush attempt, then you will benefit from QB kneel downs. And, Yahoo won't need to change anything to solve this issue.