This system is nice for just making maps, but it's not much help for making a map that serves as a tool in a fantasy RPG adventure. Fractal Terrains is at the root of the issue here. Instead of generating the world (or part of it) that you envision for your RPG campaign and/or adventure, it generates its own random world. In an RPG setting, that works only if you have no idea what you want to do in your adventure and you decide what your adventure will be based upon the world that FT generates. Lest I be misunderstood, that's OK. It's one of the methods that some GMs prefer to create their RPG adventures and settings, but it's not the route taken by most GMs.
The sample map here illustrates another problem (in my eyes, not necessarily everyone's) with the maps that FT generates. I found when I played with an earlier version several years ago that it tends to generate worlds that consist mostly of many large islands with few or no substantial continents. The sample map here is a good example of that.