It's not really a Japanese thing per se, it's a recent JRPG thing. There are plenty of Japanese games that are legitimately written for adults (the Souls games, Nier, MGS, Silent Hill 2), and in the past there were tons of JRPGs specifically that were either mature in their storytelling (SMT3, Xenogears, Final Fantasy Tactics, Vagrant Story if you consider it a JRPG) or that managed to stick the landing in the sort of Studio Ghibli "equally appropriate for children and adults" Goldilocks zone (think Chrono Trigger, Dragon Quest V, Final Fantasy IX). But the storytelling quality and target audience of JRPGs have both obviously been declining since the PS2 era. I don't really know why, but it's probably some combination of 1) perceived market pressure causing the suits to pressure devs to converge on a lowest common denominator teenage-friendly storytelling style (FFX was popular, do something like that! Persona 4 was popular, do something like that!) and 2) developers' being infiltrated by idiot otaku fans-turned-employees who destroy studios' storytelling capacity from within (sort of like how Bioware was simultaneously attacked from the outside by EA's mismanagement and from the inside by their own freakish woketard fans they hired as writers).
This is true across developers but it's also true within developers/"teams". FFVII Remake is obviously aimed at a much less sophisticated audience than FFVII itself was. Xenoblade 2 and 3 are drastically stupider games than Xenogears, to the extent that it almost sort of boggles the mind. Persona 3 is dumber than SMT3, and Persona 4-5 and Metaphor are dumber than Persona 3. Whether the audience these devs is targeting is actually stupider or just younger I'm not sure, but JRPG developers obviously seem to think it's some mix of the two. There are really very few people left in the JRPG space who are operating on the level of the greats of yesteryear, master storytellers like Yasumi Matsuno were totally driven out of the industry and the writers left at these devs can't imitate their storytelling style even when they specifically set out to do so (see FFXVI, which was obviously trying to be Matsuno-esque but failed pathetically).
That's why the best JRPG of the last two decades was just made by a French studio: Japanese devs themselves simply refuse to tell these kinds of stories anymore. It's all about the power of friendship with them, there's no room with anything else. But it's notable that this does not apply to contemporary Japanese developers in other genres - guys like Miyazaki and Kojima obviously don't feel like they have to target their games to an audience of middle schoolers or adults with bad cases of arrested development.
I actually agree with a lot of what you're saying especially about how JRPG storytelling has shifted since the PS2 era. There's definitely been a move toward safer, more formulaic narratives. But I do wonder what exactly defines mature storytelling for us as players? Is it just about dark themes like war, death, and trauma? Or is it also about how a game handles tone, character growth, and moral ambiguity?
For example, is The Witcher 3 considered mature just because it tackles adult themes? Even though the main quest has serious weight, you can still spend hours chasing goats and doing goofy side quests. Does that undermine its maturity, or is that tonal flexibility actually a strength?
Also, while I totally get the frustration with recent trends in JRPG writing, I wouldn't say the genre has gone completely hollow. We've still had some strong efforts in the last 15 years games that may not match Matsuno or Xenogears, but still push for more than just "power of friendship" Off the top of my head:
NieR: Automata (existentialism, perspective shifts, tragic arcs)
13 Sentinels: Aegis Rim (nonlinear sci-fi narrative, time travel, memory)
Tales of Berseria (revenge, emotional trauma, morally gray protagonist)
Tokyo Xanadu (grief, isolation, social alienation)
Triangle Strategy, Legend of heroes to some extent (political ethics, war, consequence-heavy decisions)
Lost Odyssey (mortality, memory, loss — from the 360 era but still stands out)
Persona 5 Royal (justice, abuse, societal pressure — flawed, but trying)
I'd argue even stuff like Xenoblade Chronicles 1 and 3 aim for heavier topics, even if they don't always land as cleanly as Xenogears did.
Would love to hear what are your own criteria for a game having mature storytelling? Is it just theme, or the tone, pacing, writing style, or what exactly?