Hi Kt,
Generally the extension fares are the same as the single fares for the zones required at the scale applying to the journey. The Fares Guide page attempts to explain what fares apply for each sort of journey. In your case you needed the zone 1 and zone 4 fares because zones 2 and 3 were paid for. Extension fares work from the boundary between zones so you don’t pay for a zone twice. On National Rail routes the extension fare might be 5p or 10p more for reasons best known to them.
Yes, if you’d used Jubilee or Northern and District to get to Richmond you would have been charged the sum of the two extensions.