Hi Xan,
Currently, the wormkit module just uses your saved settings. If you open mapgen, set all the options to random (grey ticks) and the others to how you like it and press save on the top right, it will continue to use that in game.
Obviously, this isn't great if you like variety. I have avoided trying to hijack the editors settings, as they will change each version, which is a pain. I will probably look to fibd a way to save particular settings, or at least have multiple defaults, but haven't got round to looking at it yet.