Drilled the hole and finished the Di2 build. I am still doing some tweaking. The hole drilling turned out to be pretty much a non-event. It was very easy to do. The top hole feels like there is basically zero carbon against the metal shell.
I did exchange messages with Damon Rinard from Cervelo before drilling hole and he indicated that I would not be able to go around the shell as there would not be enough room. So coming from him felt it was pretty definite.
But I did discover (too late) that you can get to the seat tube from the bottom hole for the FD. So even though there is no one that should know better than Damon I believe you can get there and pass a wire without going through the BB shell.