I'm looking at designing a mid-sized, walled port town, though it would also feature another wall inside the town at the harbour, historically to defend against any attacks from the sea (though has since become a way for the province prefect to levy taxes and duties of sailors and goods coming in to line his own pockets).  Is there any way to get one added in?

There is a tool (https://www.patreon.com/posts/city-painter-39697187) which was meant to become an editor alternative to the generator. It allows you to paint anything anywhere including any amount of walls, but it turned out to be pretty inconvenient to use, so I stopped developing it.

As far as I understand, usually people generate towns which looks close enough to what they need and just draw missing walls manually.