A-Train is the series that is basically going full-throttle with the autism, but the licensing on the Japanese end means that some content will not be available in Western copies of the game - for example, A-Train 9 v4.0 is more-or-less left to rot on steam:
while A-Train 9 v5.0 is available with community support if you are willing to jump through a few hoops and have a spare ~$178:
A-Train 9 V5.0 Final (Steam Discussion on A-Train 9 v4.0)
Another example is the western release of A-Train 8:
...and the Japanese release of A-Train 8, actually including the trains:
"Perhaps these are just decade-plus old games and licensing has improved since then?"
Unfortunately, no! One of the latest releases, A-Train: All Aboard! Tourism (with character art by the Etrian Odyssey artist), still suffers from licensing issues as the Japanese version will have more (licensed) trains than the western version of the game:
Another alternative is A-Train PC Classic:
For 100% SOVL, train otaku sisters are making their own simulator, slow going but english translation to come:
If you ever wished Train Simulator was 100% Japanese, and wanted to spend three figures and growing on licensed DLC, fuel your interests below:
An entirely free alternative would be OpenTTD and installing all of the Japanese Trains you want:
...Or if Kirsche puts emphasis on graphics over gameplay, Transport Fever 2 has enough Japanese Train mods to inflate the install size over 100GB: