Question of the Week: In regards to league rankings taking division records into account, is that an option the commish can turn on and off?
Answer: If you have 2 or more divisions, you cannot remove the best division tiebreaker. However, you could opt to move the best division record tiebreaker to the #5 position which means it would rarely be used. (If you decide to do that, you will find this setting at League Settings > Edit Tiebreakers.) The other option would be to go down to a single division which will remove the division rule altogether.
Keep in mind that commissioners can reseed the playoff teams during the first week of the playoffs if they want to have the rankings based on different (i.e. custom) criteria.