Hello Michael,
Jim is correct. I will say it in a simpler fashion just so it is clearer, if needed.....
If you are using your nanovna to do antenna fine tuning so that you can hook it up to radio and use it - then do your calibration on nano and then measure at the coax right where it plugs into the radio. This will give you the swr over the coax all the way to the antenna. Do your adjusting on the antenna until you get an acceptable vswr level that you want to hook up to the radio. Then unplug the nano, plug the coax into the radio (or tuner) and away you go.
If you are building an antenna or balun or unun then just measure at the connector of that device and build to what you are looking for.
So, both of you were correct in your statements.
Hope this helped.
73
Mark