The UI also keeps a list of free pins:
https://github.com/OpenSprinkler/OpenSprinkler-App/blob/master/www/js/main.js#L4898
so if you need to change the free pin list, you will have to change both the firmware as well as the UI. You can certainly clone the UI, change it, and run it locally (just double click index.html to launch the UI). Another work-around is to use HTTP API to send command to the controller manually to set GPIO zones. This allows you to bypass UI so you only need to modify the pin list on the firmware side.