I am just not a fan of micro managing the line up based on who is pitching. It just doesn't make a big enough difference. IMO, it might do more harm than good having the batters hit in different line up spots from day to day.
That said, the decision should be based on the player's comfort level in a certain spot, and also the comfort level of having a consistent spot versus being moved around. As we've mentioned many times, I'll trust Cora to know what's best.