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Rather than Y cable, can’t you just wire one shifter to the other, one cable to the junction box and one cable from whatever free port to the internal junction A cable? No soldering needed.
Didn’t think Di2 was fussy about where things were connected, just that they were connected.
I think this is how I wired mine in my Superzero bars (which are awkward as they have a cable channel under the tops, but the only way you can go internal is through the drilled holes near the bar ends)
You need internal and external junction boxes and 2 cables for shifters the rest sounds fine