Is it possible to mount Shimano Ultegra 6870 Di2 on a 2012 Cannondale SuperSix?
I wouldn't modify a carbon frame as it'd be difficult to detect the beginnings of delamination where you drill it.

Internal wiring is optional. You'll need an SM-JC40 for external wiring, a SM-BTR1 and SM-BCR1. The charger which connects to the front junction will only charge internal batteries.