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Everything in tf is relative. There is no absolute position, so nothing is at 0,0,0.

TF only describes transformations between different frames. In your case base_footprint and base_link. The footprint is "on the ground" while the base_link is setup a little bit higher as the wheels make the robot a bit above the ground. That's the only thing that you see in the tf output.

As this is relative, if you'd move the robot in gazebo, the transform will also stay the same.

Of course gazebo has to have some global coordinate system, but that is independent of tf, unless you anchor a fixed frame at gazebo's world frame.