I have the same 785 shifters on my tandem, but I routed the wires inside the bar and used the bar-end A-junction. Those shifters only have one port, but that shouldn't really matter. With the external junction A you need 6 wires - one from each shifter to the junction, one from A to B, then one to each derailleur and to the battery.
I posted about my di2 hack on the forum below. Not something everyone would want to do but it actually worked out well.
di2 Hack
I think you will need the B-junction in the seat tube, and it will still need enough length below it to be able to remove the seatpost without pulling all the wires apart.