It's primarily the latter: it best maximizes Kanter's strengths and minimizes his weaknesses having him come the bench. Would you rather have Kanter guarding an Austin Rivers-Cole Aldrich pick-and-roll or a Chris Paul-DeAndre Jordan pick-and-roll? Would you also rather have Kanter going against Cole Aldrich or DeAndre Jordan on the offensive end?
Not to mention, the Thunder's three best players have all come off serious injuries in the past several seasons, so the team is looking to lighten their individual workload. Not ideal to have Serge constantly having to cover for Kanter after two consecutive seasons of lower-extremity injuries.
Finally, the Thunder's starting lineup of Westbrook, Roberson, Durant, Ibaka, and Adams was fairly productive last season: +15 net rating with a less-than-100% Durant and two new starters. Not unreasonable to think the starting lineup is effective enough as is and could stand a good chance of being even better with some good health and another year of chemistry.