Hi @FraSec, welcome to the forum 
The design Kevin presented here is specifically using only fixed-orientation thrusters, in which case a build of ArduSub with a custom frame should be sufficient for controlling it, provided it has sensors that allow it to estimate its position and the like.
If you’re after a more traditional AUV design which makes use of control surfaces then that is not currently possible with ArduSub, and developing a compatible version may be more challenging than adapting a firmware like ArduPlane to work underwater.