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I don't have an answer to your actual question (why setting a goal in the base_link frame doesn't work as expected), but some clarifications regarding the odom frame:
It seems the odom frame is following a x-right, y-front coordinate system. Is there a 90 degrees rotation between the two frames?
That changes over time. The idea is that if you set odom as your fixed frame in Rviz and move your robot, you should see your robot (base_link) moving around, according to the odometry information. So yes, if your robot turns by 90 degrees, there will be a 90 degrees rotation between those frames.
The current rotation/translation between odom and base_link is easy to verify by enabling the TF visualization in Rviz.
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