Jamie Thompson wrote:

I've still not heard a good argument why someone would get off a fast
train at Clapham Junction to take a slow tube to Waterloo....where
that fast train was going anyway.

If it's anything like Stratford & Liverpool Street, part of the attraction
is that you're more likely to get a seat if you board at Stratford, plus the
connection at Stratford is easier. I assume a Clapham Junction tube station
would have a better layout for interchange than Waterloo, although obviously
it won't be cross-platform interchange with metro services.