Anyway, is it necessarily the case that if pre-pay were introduced on
NR, the fares would have to be the same as tube fares? Would they have
to be zonal at all?

I would imagine part of the "discussions" between TfL and the TOCs is
about this. If they introduce a different system of fares for NR it will
mean increased costs to program the Oyster system, the system will
also be more complex for users and will be far more complicated to
update when fares change. None of this is desirable to TfL or users.

How would the system cope with changing from a line on one tariff to
another or the tube or DLR without even more of those on-platform
validators? Plenty of interchange opportunites exist. Would you be
charged differently if you don't validate half-way. Would anyone
understand when they need to and when they don't? Most people do
not understand if they need to at the start and end of their journey let
alone the middle.

Was a special deal with the relevant TOCs needed to get pre-pay
introduced (including £2 evening/weekend singles) on routes such as
Upminster to Fenchurch Street, and especially Harrow & Wealdstone to
Euston (where tube single/return paper tickets weren't and aren't
valid)?

The special deal already existed for Fenchurch-Upminster. British Rail
(and their successors) had agreed to accept all tickets issued by London
Underground and vice-versa from long ago so Oyster is just another form
of LU ticketing which comes under that agreement. Some agreement must
have been made for the sale of Oyster in the c2c ticket offices though.