I think building a full bike and then cutting it and inserting the carbon tubes makes senses. It allows Cannondale to continue to use thier existing jigs, and it ensures that the frame will be in alignment when the carbon is added. It is very difficult to build the lugs seperatly, especially the large lugs that Cannondale is using, and a have them all come out straight and complementary.
Superlight, where did you hear that the holes in the head tube are for air bladders? I expected that the carbon tubes came preformed and were simply glued in and would not need any extra pressure to complete the bond and force out excess resin. I wouldn't worry too much about water entering the bike. It happens to any bike ridden in the rain, and the aluminum won't have the same rust problems of a steel bike. Any bike that is welded together has breather holes in every tube, usually hidden inside a joint when possible, but water can still enter and exit from these holes.
First of all, the six13 isn't lugged, it's a aluminum frame with sections cut out and carbon put in its place.
Secondly, I heard the holes were put into the head tube by a cannondale rep that brought in the six13, I mentioned that in my original post. What did you think they were they for?
Third, the carbon in the frame are not merly carbon tubes bonded to the aluminum, the carbon is inserted inside the frame while wet, then the holes in the headtube are used for inserting the air bladders. Keep in mind the whole frame is put inside a mold, in which the air bladders air filled, extruding the carbon into the aluminum, making a seamless carbon/aluminum bond, both mechanical and glue.
And lastly, I would worry very much about water getting into the head tube, not so much of the frame corroding, although as Ye Ole Balde pointed out it can happen, but mostly it is a problem because water will get into the headset, ruining the bearings.