Cubik Studio

I know they are hardcoded into the game code itself but Qubble allows it and I really think that such feature if it's present into a freed (and a bit crappy imho) modeler, there is no reason why a more developed software like cubik should't have it.

That tool is a Mod and has access to hardcoded things. Minecraft entities are hardcoded and so accessible by a Mod, not a thirdparty software.

However, Minecraft will probably has a good way to modify Entities in a future update (it's already possible in MC PE for example).