Contrary to what some may tell you, it is possible to use a regular road bike with clip-on aerobars and be quite successful in TT's. While you won't be as fast as you can be with a dedicated TT bike, you can be fast enough. You just need to practice and train well.
As for shifting, I wouldn't worry too much about setting up satellite shifters. If you find that you need to shift gears, just take your arms out of the clip-on's and shift, then go back into the aero position. Granted, being on di2, you could do the shifter bit substantially easier than guys with mechanical systems, but you'll probably find it's not necessary.
BTW, you'll be required to take the aerobars off for any mass start events.