..one may not consider that aa shell behaves as if all the mass on the shell were concentrated at the shell center..
Why not? This is simply a geometrical approximation, which becomes more and more relevant, as the distance increases. At the very large distance scale such shell would behave like pin-point object with respect to gravity spreading. Try to draw image bellow at scale and you'll see, why Newton could use it for derivation of gravity force between Earth and Moon without excessive simplification.
..the shell theorem is described as a "proof" that ..
Nope, it's a geometrical approximation (..a quite trivial and apparent, IMO..), which Newton has used for estimation of gravity force in spherical geometry - no less, no more. In more detailed analysis we should use a more exact approximation and Mr. Newton realized it too a quite well. For more exact derivation of gravity force near sphere please check the article
here and
here.
