This is just anecdotal evidence, but I feel like residence card checking has kind of cooled off in recent years, at least in Tokyo. In the "old" days, (ten-plus years ago) I just remember it being something you'd expect to happen from time to time -- a natural "disaster" kind of like an earthquake or typhoon.
This came to a head for me during a period of time -- I want to say it was about 8 or 9 years ago -- when I had my card checked three times over the course of like six months, all in Tokyo's Suginami-ku (specifically, Asagaya and Ogikubo stations on the Chuo Line). No idea if they were on some "overstay alert" at the time, but I remember being genuinely incensed/insulted, especially because of the miserable timing of all of them -- one was when I was on my way to a friend's wedding and another when I was heading to a hot yoga class after a stressful day at work -- and because of the smug way the officers behaved during the former ("Sorry, but I'm on my way to a friend's wedding and kind of in a hurry." "Ohhhhh, well we can just have a friendly chat along the way." Yeah, **** you.)
During the third (and final time), I tried to remain calm, but really genuinely tried to express how insulting it was -- having lived here for multiple years and coming to this neighborhood every day, to be treated like a criminal (or suspicious person at best) in a public place where my yoga teacher or whoever could see me. (I also made a point to explain how hypocritical it was because an Asian-looking person could just as easily be a "foreigner" overstaying their visa, but they were ostensibly not randomly stopping them.)
Anyhow, for better
or for worse, that was the last time I've ever had my card checked -- literally haven't even been approached by a cop maybe eight years running now. (Sometimes I honestly wish someone would check it now that I have permanent residency, just so I could show it to them, shake my head, and be like...really? But on second thought, nah, no I don't.

)
I don't think for a second that my rant had anything to do with anything (though I hope it, if nothing else, gave those two officers some food for thought), but I wouldn't be surprised if somehow people at the top gradually realized that this trend of treating anyone who "looked foreign" as a potential criminal was maybe -- just
maybe -- counterproductive to the Japanese government's stated goal of encouraging more tourism to/international interest in Japan.