Do you know how politically complex it is to build a single high speed rail line? In one country? Its so mind blowing complex politically, its almost unfathomable. And even then often it only results in an upgrade of an existing line, rather then a new line.
Building a whole new infrastructure from the ground up, would not only be absurdly expensive, it would also be absurdly impractical and take literally 50 years if it would ever happen.
Yes, Japan is correct that sometimes, more separation is a good thing if your network can be simpler.
But at the same time you can't just reverse that and then conclude that 'lets make everything as different as possible' and believe that's somehow going to turn into an efficient system.
We can not just simply ignore 200 years of train history and evolution each countries system has. I'm all for learning from Japan, but we also can't and shouldn't just copy Japan.