|Honshu side entrance of the Seikan Tunnel|
Okay, so here's one interesting potential solution to the problem. Japanese freight trains are narrow gage with a limited clearance profile small enough to fit on a flatcar and still conform to the clearance profile of the largest Japanese high-speed train. The train-on-train concept is exactly the above. Why not load the freight train onto a faster moving freight train in the tunnel and speed up the entire operation? I can't find a lot of details (but at least there are 2 pictures on Wikipedia, hooray), but I'm sure there are quite a few technical hurdles that will need to be overcome. We shall see what comes out the other end eventually.