But is it the only exception? Trains from Marylebone to Wembley Stadium
are shown alongside Finchley Road and Wembley Park stations. Southern
trains are shown calling at Willesden Junction (that's just plain
wrong). Tottenham Hale Hackney Downs is shown away from Clapton. The two
Bethnal Greens are shown on the same formation. Trains that avoid
Lewisham are shown avoiding St Johns as well. Trains from Brixton to
Victoria are shown nowhere near Clapham High Street and Wandsworth Road.
Watford High Street. c2c trains are shown nowhere near Bromley-By-Bow.

No comment on most of your list, but trains which avoid Lewisham do indeed avoid St Johns as well, because there are no platforms on the 'avoiding' lines.