You’re probably seeing some of the oversensationalized ultranationalist garbage coming from that loud minority (and their loudspeaker vans), as some of the supposed incidents involving Mainlander tourists are isolated cases. That afaik there are fewer “locals-only” izakaya and exist only in rural areas or lesser known urban areas (but even then you’ll have to look out for some pushy touts and bars charging too much for anything on the menu).

You should be fine using other guides to know where better to go to, such as Atlas Obscura.