Yeah the position of an element in the physics engine (Farseer) is based on the location x,y being at the center of the object.
You could get at the UI Element of the physics object and get its position instead:
Ellipse ball = _physicsController.PhysicsObjects["ball"].uiElement as Ellipse;
(there is an example of this on the main wiki page if you need more info)
But I think what would be best for that is to add a property to the Physics Object Behavior that wraps a Sensor in the Farseer Physics Engine.
Farseer supports Sensors, and I think its actually simple - you just set the IsSensor property on the Geometry object to true, and then that object will fire collisions, but does not move or have impulse, etc.
You could try to do this manually, again by going through the PhysicsObjects collection and getting the Geometry object, and setting IsSensor (sorry I haven't tested this, might be wrong!)
_physicsController.PhysicsObjects["ball"].GeometryObject.IsSensor = true;