It's possible the following is fundamental to Unity, and not a problem?
I am using an example of a WheelJoint2D/Car from the Ray Wenderlich tutorials. Note from the pic below, the top level game object called "Car". It has children of "Body" which contains the wheel joints and the wheels (attached to the wheel joints). The top level "Car" GameObject is placed in the scene (here at X=6.4).
Now we run the game for a short time, and the car rolls forward as expected. From the inspector, we would see that X position of the Body and the wheels has changed, but note that the Car game object's X position has not changed:
So, in reality the game object "Car" has grown in the X-dimension. Granted this growth seemingly has nothing to do with physics simulation (as all the rigidbodies and joints are moving along as expected). One interesting side affect is that this growth might make scaling the parent object problematic.
But it seems that if this were an infinite runner, you would have an ever increasingly wide "Car" object. On the surface this seems undesirable, but is it really? And if so, how would you mitigate this (given that this game object hierarchy seems to be the prescribed way of using the wheel joints).