The Globemaster has always officially been the C-17A to the USAF, and the use of C-17 only is probably down to laziness.. I believe the last aircraft to enter US service without a variant suffix was the B-29. Every aircraft since has had an 'A suffix even if only one mark was ever used. Examples include the TF/F-102A, F-21A, B-2A and C-29A.
The reason given for not designating the F-4J(UK) as the Phantom F. Mk.3 was seemingly to avoid confusion with the Tornado F. Mk.3, which was not far away from entering service. I can't see the confusion myself; one was a highly capable, well armed interceptor and the other was the Tornado. Sorry, hat and coat etc...
I believe that the MoD recently officially dropped the 'II' in F-35B Lightning II.