There is an OSI between Waterloo and Waterloo East, so that is pretty much the best example for that fare.
When the Oyster fares were originally set up for the 2010 expansion of PAYG there were a lot of redundant routes put in just in case. In those days pretty much all Oyster fares were solely within zones 1-9 (only Watford Junction and Grays existed beyond that). I agree that in this specific example routes going beyond Wimbledon are pretty pointless. If someone really did want to go from West to East they would probably buy a ticket via Epsom, or take the bus.