The existing rail network is already pretty jammed on a lot of lines. Cargo does run at night (mostly) on other rail lines, but night is when maintenance is also done (we don’t really have any 24-hour trains here except on special occasions and I think none of those even since corona). The safety record here does come with a cost in that sense; the checks, maintenance, and construction all occur at night with freight running around that.
If they are adding this in the middle of the expressways, the land is already acquired. It probably takes less infrastructure to do this than putting in rails would involved. I also doubt it would be to code for rails since there needs to be room to get passengers off in the case of emergency, etc. Zooming in on 35.698190871019335, 139.75230458261458 in Tokyo does show there isn’t even really any room between lanes, though, and it’s not different up where I live a few hundred KM north so I’m not exactly sure what the play is. All expressways are paid today and the tolls were supposed to go away eventually, but they never will if the construction never ends (and it never ends).
People didn’t find what they wanted and/or went back to what was stable and familiar. I still am avoiding using reddit for anything except the subs related to people living in Japan (the community didn’t move over; a couple did but there were basically no posts very quickly) and when it shows up in some search result and nothing else has worked.