It is pretty hard to mod a Unity game. Unlike other game engines that load game balance values and art assets from public file types (like .png, .obj, and .txt) Unity bundles all assets into a propriety file type. Muse would have to make a special external file loader to make modding possible in the traditional sense.
That said the Unity Engine is free to use for indy development. You could create a game from the ground up with the same mechanics of Flight of the Icarus.
What aspects of the game did you want to mod anyway?
