Did you set a variable WHITELIST ?
Mine contains: 192.168.*.*,127.0.0.1,172.*.*.*
Andy is right, the whitelist gets overwritten, other settings can be changed in the settings file, but the container has to be stopped before.
Are you sure the vpn is connecting now?
You could try doing "docker exec -it Transmission ps -A" to try and see if Transmission is even starting. Could you try that and post the result and a new debug log?