Being, like you, a neat freak, I managed to get most of the wiring in my Trek's down tube. I drilled approximately 9/16" holes and used a fish tape to pull the wires after putting on rubber grommets. I just don't like having bundles of tie-wrapped wire hanging off the frame. It REALLY cleans things up.

The connector that is a supplied Y splitter cable that connects to the motor's/controller lead to the display/brakes/throttle. It is about 13 mm thick at that connector. The additional connections to the switch for / lights / horn are all hard wired with again, each with 13 mm thick watertight connectors. I don't see how you could easily do it internally inside a frame. Maybe splicing / reconnecting all the wiring bit by bit? I'm skeptical it's worth it. I like mine a lot, works great, but yeah it would be nice if I could run it inside a frame. I suppose it would depend if you can fit something that thick (13mm) into your frame. As an aside I find I still need to run additional lights for night riding beyond the 300 lumens (or so) that the kit's headlight provides.