While that applies in the case of the 03 series and the 6 door cars, you can't exactly take limited express trains out of the major commuter lines.
The problem with that is that the existing tracks are so close together that the Shinkansen has to be slewed over no matter what. And there is a bridge over the tracks at Tamachi station that would further increase any high bridge.Don't think that's going to happen.
The freight/Haneda Line is about the same elevation as the Shinkansen spur leading to the depot. It shouldn't be too difficult to ramp it over the existing tracks, on a high bridge through Tamachi (like the Ueno Tokyo Line structure around Kanda), then ramp down just before Hamamatsucho/Shimbashi.