I have contacted GTR customer service. The response was that I would need zone 3 for my Travelcard. I then asked again about the route I intend to take and the response was that the ticket “isn’t expected to be valid” through Waterloo and Clapham Junction, which means a “loophole” has been brought to attention.
I am not responding further and depends on price difference, I’ll try to avoid this route or buy a ticket from West Hampstead Stations to avoid the problem.