1) It’s too close to Liverpool Street. If it was zone 2 then a lot of commuters from the East and South would travel there rather than into zone 1.
2) Essex Council provide a financial contribution to allow the whole end of the line to be in zone 6. It’s a similar situation to Caterham, Tattenham Corner and Epsom Downs in Surrey which all used to be beyond zone 6.
3) Watford is down to usefulness of service and time to Central London.
You might find this video https://www.youtube.com/watch?v=do2tNpuYFM0 of interest.