I spent a while looking into this and it looks like it's mostly legit. Japanese stations really do seem to be bigger. Having said that, there are two big caveats that make the gap smaller.

First, they're double-counting a lot of passengers in Japan. Tokyo subway isn't a single thing, it's a collection of independent companies, so you need to tap out of one station and tap back into another when changing lines. The JP numbers on Wikipedia are the sum of all the separate Shinjuku stations, which would count a lot of transfer passengers twice.

And second, the table is counting Tokyo's metro system but doesn't include Chinese cities' subways. There are no subway-only stations listed even though plenty of them meet the 30 million passengers/year cutoff. But that's not as big an issue as you might think because even the busiest ones are still far smaller than the big Japanese stations - The busiest is Xizhimen with 237,000 passengers per day, which would translate to 87 million per year. Beijing South Station's subway stop gets 211,000/day = 77 Mn/year, so if we added that the rail passengers it would bring the total to 318 million - but most of them would be going to/from the railway station so that's doing the same sort of double counting as I mentioned in the previous point.

Source for Beijing subway passengers: https://xinwen.bjd.com.cn/content/s684153bfe4b0380e186d0b6e....

Shinjuku being as concentrated as it is, is mostly a historical accident. Prewar Japan prohibited mainline railway options inside the Yamanote ring, because old steam railways took up a lot of room with yards and were very polluting; and and so you have all the suburban and long distance railways stopping or going around the ring (the notable exception being the Chuo Line which was built before that regulation). And the flattest, largest, and most attractive land development areas were west of the Yamanote ring so most trains ended up at Shibuya, or Shinjuku, or Ikebukuro, which round out the top three stations in Japan. This led to a lot of problems as these stations became more overcrowded with people changing from mainline suburban trains onto local transportation services. The through-running subways of Tokyo were developed largely to fix this, by allowing trains to pass through into the formerly prohibited city center so that people would stay on the same train instead of clogging up the platforms and stairwells and passageways by transferring. As more railways were able to through run, that lessened the need for yards to store trains that were no longer terminating, and they became large parcels of redevelopment that begot even more ridership.

To some degree, future planners learned from this by not overly concentrating passenger flows at a handful of stations; and by the time they were rapidly urbanizing, trains had become electric and there wasn't really any good reason to stop trains from entering central cities anymore. If you look at the Seoul or Beijing or Shanghai networks, they are intentionally a large, overlapping grid with many transfers to reduce the load on any single station.

I think you forget to take into account how centralized Japan is. Tokyo is not only the biggest city in the world. It’s also extremely centralized in terms of its infrastructure and as much as other Asian cities have developed similarly, they have also developed more recent and with a different urban model. It’s unlikely that the hub system used in Japan will be replicated somewhere else on that scale.