Using the conference record to break ties would emphasize the division of leagues into two conferences. That separation is already done for scheduling, the all star game, and playoffs. Since what we are talking about is a ranking withinconferences, it is reasonable to include conference games as a tie-breaker.
The conference record is easy to visualize - see any newspaper that covers the NBA. Point differential is rather hard to to visualize, especially when dealing with 4 digit numbers. Point differential is of course useful as an ultimate tiebreaker due to the unlikelihood of teams ending up with the same point differential.
I am not advocating use of head-to-head, simply because it is more difficult to program, and because only two games are played against conference opponents, it may often not resolve ties.
Do those those Other Popular Manager Games use conferences?