I think it's more politics and economics. Switzerland is quite a lot richer than Japan and is extremely decentralized politically. That creates strong incentives to provide good public services even to mountain villages. It also helps that Switzerland isn't experiencing population decline. The Swiss population as a whole is growing quite rapidly and from what limited data I could find even rural regions are growing. I think land acquisition doesn't really play a huge role. They are both mountainous countries where rail projects have to squeeze in valleys or bear the expense of tunnelling.