Not going to lie, I know nothing about programming and Sunless Sea seems to be pretty hard to mod, yet I would love to know if it would be possible to take the engine and overhaul it to make a different game. My idea would be called Scorched Soil, a game set in a nuclear post apocalypse in which you cross the wasteland in your car and travel to the different settlements and areas. Fuel and supplies would be the same, but instead of Terror you would have Heat, your vehicle would have a cooling system instead of a light source and if you travel across the desert without your fan on well, you will start getting hotter and hotter which could ultimately lead to your death. I have several ideas thought, mostly about places to see and visit. In case people gets interested in this and the users tell me that it is possible I will reveal more information.
Might I suggest you check out A House of Many Doors: http://www.pixeltrickerygames.com/
That wouldn’t be possible with the modding functionality. You’d have to actually alter the game’s programming, at which point you’d be better off just making your own game from scratch.