I am not Di2 yet; that is next on my upgrade list. I do not know if I will put the junction box in the Alpha X compartment or the IA16 compartment on the front of the head tube. I will probably put mine in the Alpha X, but I am not sure what is easiest for charging access.
The other thing I want to investigate is whether I can use this in one of my extensions and then permanently hide the junction box. But, I would only do it if I can figure out a clean way to route the Di2 wire if not through the end of the extension.