https://automaton-media.com/en/news/konami-is-intent-on-region-locking-japanese-players-out-of-metal-gear-solid-rising-revengeance/
The July 4 GOG.com release of the 2013 action game was promptly made unavailable in Japan moments after launch
Bottom line: Konami is a weird company making odd calls and has been for a long time. Someone in charge likely decided 11 years ago that MGRR should not be released on PC in Japan and that's all there is to it.
This has happened before, for games from other publishers, as per the article. I don't remember all of the reasons for it, but if I'm not mistaken, this is why Shogun: Total War 2 has a blood DLC for a few dollars, so that they can make everything but the DLC available in Japan.
That's Australia. They have weird anti-violence laws, and God-fucking-forbid anyone learn that blood exists. I think their stupid drug portrayal laws are why the first Fallout had to call them "chems" instead. It's all pretty stupid moral crusade bullshit.
I suspect Australia is responsible for Streets of Rogue changing "cocaine" into "sugar" as well, but I know Japan doesn't allow things like beheadings in their games, which I thought was part of that DLC.