Bell's warning concerns the order of explanation. A formal change of coordinates can be mistaken for a physical mechanism, or for a proof that ordinary questions about material rods and clocks have become meaningless. In the cited essay he recommends first following a concrete model's equations of motion, so that changes in a moving system's shape and period are understood before a general correspondence between frames is used. The phrase quoted in the question occurs in note 10, following the discussion of a classical charged-particle model.[ref]
A useful independent diagnostic is to ask whether a proposed account predicts an actual stress. Consider two ships with identical acceleration schedules in one inertial laboratory and a fragile thread between them. Their laboratory separation remains fixed. Once both coast at speed , the separation of the attachment points measured in their final common rest frame is , where was the fixed laboratory separation. A thread whose unstressed rest length is must stretch to span those points. For a sufficiently fragile thread it breaks. Saying merely that all contraction is a matter of description misses a mechanical consequence of the specified history. Conversely, length contraction is not an additional universal force pulling every object shorter regardless of its constraints: the stress response depends on its material dynamics and acceleration programme.
The same methodological point applies to clocks. Their ability to realize the relativistic time standard requires compatible physical laws. Calling a variable a new time coordinate does not by itself explain why an atomic transition, an oscillator and a material measuring instrument behave consistently with that variable. Lorentz-covariant dynamics can connect these descriptions without introducing a second set of observable clock readings.
Bell's lesson need not be inflated into a rejection of Einstein's principles or of Minkowski geometry. His comparison expressly recognizes the power of the principle approach and does not require adopting an empirically preferred ether frame. The defensible caution is that covariance, observable physical behaviour and an ontology of spacetime are different claims. Geometrical explanations are useful when their connection to matter and measurement is understood; premature philosophising begins when a coordinate transformation is made to settle those further issues without argument.