That's only on Switch/PS4/PS5 btw. The game is also on mobile, which is huge in Japan.

No big updates the past few months besides Minecraft's lead widening by another 200k or so.

The latest seemingly notable candidate for this list seemed to be the Mario vs Donkey Kong remake, since it is developed by the Seattle-region-based Nintendo Software Technology. However, it appears that the remake will ultimately sell significantly less than the series at its height on the DS, barring impressive legs.

Also note that Marvel's Spider-Man 2 fits the category of "games that might be on the list if we knew digital sales, with almost 300k confirmed retail sales.

Minecraft Game Pass redemptions are not included I take it. I don't think subscription redemptions of titles on PS Plus or Game Pass are ever included in generic digital sales.
I'd have to imagine a good number of the Game Pass subscribers in Japan downloaded Minecraft.
If Minecraft ever gets native PS5 and Xbox Series X/S versions, I don't think you'll get too many double (or more) dippers in Japan or globally.

July 2024 Update

• These past 4 months, Minecraft had about another 80 thousand sales on Switch. By the end of the year, it will likely surpass the combined sales of entries 2, 3, and 4 on this list combined.
• Luigi's Mansion: 2 (Dark Moon) HD has just charted its first week in Japan with 88,425 sales. This is enough to push it from the #8 spot to the #7 spot. The game is likely to continue selling well, seeing how the 3DS port of the original Luigi's Mansion had a FW of 29k and lifetime sales of 101k (similar figures for LM2HD would place the game at about 300k sales on Switch, for a combined total of 1.61 million).

Looking Forward

• Despite Donkey Kong Country Returns being knocked down to 8th place, the planned port of the game for Switch in 2025 should chart decently. How well it will sell is a bit hard to judge, since it is being released so late in the Switch's life, is competing against a newer DKC game on Switch, and seems to be highly priced for an updated Wii game. That said, Tropical Freeze sold over 240k retail copies on Switch alone, so there is clearly a fanbase present.
• Assassin's Creed Shadows is arguably unlikely to enter this list, seeing how the Assassin's Creed series doesn't do especially well in Japan. On the other hand, Sucker Punch's Ghost of Tsushima did far better than their prior Infamous games in Japan, so there is precedent for a Western developer attracting more sales in Japan by adopting Japan as a setting. Even if Assassin's Creed fails to break similar ground, that is newsworthy in of itself.
• Grand Theft Auto 6 is going to be a massive worldwide hit when it comes out, and Japan is part of the world. More seriously, GTA5 is the #6 game on this list, so it's reasonable to assume its sequel will do very well.
• Given that PC gaming is doing reasonably well in Japan in recent years, it is likely that Ghost of Tsushima will sell many more copies on that platform. However, barring another major milestone, we'll probably never get concrete numbers.