The Unity version has by far less features and is also way slower than the Standalone version. Also, the Unity version is meant to create terrains within Unity only.
The Standalone version has tons of more features and it is meant to create terrains that can be utilized in many other applications as well (e.g. Unity, Unreal, Cinema4D, 3DS Max, Maya, Blender, Houdini, Quixel Mixer, Substance, Photoshop, Cry Engine, Lumberyard, Vue, Terragen, Clarisse, Octance, and a lot more). Beside that, the Standalone version is a pure GPU terrain and landscape creation tool. Hence, everything you do, you do it in real-time (you see changes instantly).
The Standalone version replaces the Unity version entirely. We decided, that the Unity version should no longer receive new features and updates. That way we can fully concentrate on the development and maintenance of the Standalone version, which is the way more powerful version.