From what I read, the Kaguya clan (Kimi's clan) was stated to have attacked Kirigakure, not that they were from there. 
Though, lol, there isn't a bone village so Kimi could have fit in anywhere. That is not an elemental technique nor does it really relate to any element as it is biological. If he could grow and sprout plants or turn his bones into stone that'd be different. But bone could fall into any element. Especially if you consider that bones are full of stuff like blood and squishy stuff and white blood cells. Physiologically, it could really fit in with the mist village all the same as the Byakugan fits in with the Leaf :0