the absolute encoder center position does not matter so long as the extents of a given axes are 0<4096. When you calibrate, the center will be exactly 1/2 between the endpoints. That number becomes center, not 2048.
If your stick is not perfectly centering inside the blue circle, it is likely because your grip weight plus any extension offset is dragging the stick away from center because it isn't balanced.
Use the balance force feature + adaptive recentering to counteract any imbalance in the weight distribution of the grip.