If the whole journey you are making includes NR elements, then any extension fare will be at the NR scale, even if the extension is not on NR services. If there was another way I’d tell you.
As for using Whitechapel or Canada Water rather than London Bridge, I don’t know but it may well be a similar time. There are more ELL trains at Penge West than Southern and you have extra services joining at Sydenham. My best advice is to try it out.