You are right, it is not specific to software, just wanted to add more context and also, because I don't know the answer and I believe there are multiple factors, but my two cents: a mix of history and culture.
By the time software came around, Japan already had a well stablished manufacturing industry that had a reputation for quality (this wasn't always the case).
Software was something totally new and wasn't considered important, why? perhaps management didn't understand it or didn't know how to handle it and did nothing.
The above made a career in software not very attractive compared to other industries. Since then, companies struggle to get good developers, who can move to more attractive sectors or countries than trying to change things within Japan with its rigid hierarchy.
How things move in Japan is generally by someone breaking the status quo and the rest following if it is a success. That was the case with Toyota in manufacturing for example. For software it hasn't happened.
Another problem IMHO is that code is invisible to users. If the app works, people don't care if the code is beautifully made or not, and without consumer pressure, management doesn't care either. Compare that with the complains they'll get if a physical object had the sightless defect.
Finally, there is a higher entry barrier for physical products than software. Any teenager can build an app in her bedroom, it is a different story to develop a bullet train. Inefficiencies and slow decision processes in manufacturing are less obvious than in tech (though manufacturing industries in Japan are struggling as well because of this), and Japan simply isn't competitive in this area, making it less attractive to invest.
And perhaps, the most important: People got used to it and don't have higher expectations.
By the time software came around, Japan already had a well stablished manufacturing industry that had a reputation for quality (this wasn't always the case).
Software was something totally new and wasn't considered important, why? perhaps management didn't understand it or didn't know how to handle it and did nothing.
The above made a career in software not very attractive compared to other industries. Since then, companies struggle to get good developers, who can move to more attractive sectors or countries than trying to change things within Japan with its rigid hierarchy.
How things move in Japan is generally by someone breaking the status quo and the rest following if it is a success. That was the case with Toyota in manufacturing for example. For software it hasn't happened.
Another problem IMHO is that code is invisible to users. If the app works, people don't care if the code is beautifully made or not, and without consumer pressure, management doesn't care either. Compare that with the complains they'll get if a physical object had the sightless defect.
Finally, there is a higher entry barrier for physical products than software. Any teenager can build an app in her bedroom, it is a different story to develop a bullet train. Inefficiencies and slow decision processes in manufacturing are less obvious than in tech (though manufacturing industries in Japan are struggling as well because of this), and Japan simply isn't competitive in this area, making it less attractive to invest.
And perhaps, the most important: People got used to it and don't have higher expectations.