Have seen the same behavior with
CollisionShape2D set to the predefined concave shapes (rect, capsule).
Ended up using
RayShape2D, as it pulls the player body out of the static colliders.
My guess is that physics engine does count your collision and stops the
RigidBody2D, but the processing steps are discrete, so you see the bodies overlap.
Edit: Downloaded your source, you have scaled the CollisionShapes. That should always be 1,1