Waterloo East is as you say and has been for generations (perhaps right back to the 1920's?)
New Cross - the NR running lines are numbered 1-3 (since the last resignalling) but if the platforms were so numbered, the ELL would have to be 0 - I think that's the reason there.
Catford is a recent change (doesn't show on the SR Track Map) - a spin-off of the internet/mobile app age? Or do the departure indicators at street level show both stations in one? Not been there in years so don't know....
I have also read the justification that it avoids confusion if emergency services need to be summoned