odom not aligned with base_link?

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The odom frame is a "world-fixed" frame. The (0, 0) point in the odom frame is where your robot was when you started it. So if you turn your robot on, and drive 10 meters forward, then turn left 90 degrees, and then drive 5 meters, your robot's pose in the odom frame is (10, 5) with a yaw/heading of pi/2. The odom frame will not move, because it is "fixed" to the world, and not your robot. The base_link frame is fixed to your robot, so it will move as the robot moves. Note that your robot's pose in the odom frame is equivalent to the odom->base_link transform.

For more information on coordinate frames in ROS, see REP-105.