Maybe that’s just me but I don’t think of Japan as a bad model in how to have a dense population that is prosperous. If anything their biggest problem currently is depopulation of remote areas.
It's an incongruous question. Hyperloops between Basel, Bern and Zurich would make them into one virtual Mini-City. The loops would also reduce density in the travel corridors preventing a California catastrophe kind of sprawl inbetween.
Basel<>Bern (direct) would need tunnels.. The other 2 routes are pretty flat. Most of the Swiss economy is in the valley between the Jura range and the Alps.
The necessary tunnels for Basel would probably cost less than this: