Nice map … except the extension is going the wrong way.
The zoning issue is going to be a nightmare locally on the ground. You could come out of Sainsbury’s and pop next door to zone 1 Nine Elms station, or walk half a mile towards central London and board southbound trains from Vauxhall in zone 2. I think it’s likely that the stations will start in zone 1, but I wouldn’t bet against them becoming zone 1/2 in the future.
As for the map, the only way it will work sensibly is to put the extension over the top of Vauxhall. There are other places where stations are not in the correct place on the current map (eg the two Bethnal Green stations). The dotted link to the pier from Vauxhall will have to cross the extension line, but that’s probably the least worst side effect. Alternatively they could just lose the dotted line and put the boat symbol by the station name as they do at London Bridge.