I found it hard to get passed the poor writing style and journalism... "Kicking it off was the Mayor of Osaka, the son of a yakuza boss, who as most yakuza are, was probably heavily tattooed"???
My experience has been that almost all "public baths" allow tattooed people since they are "public." There are still many apartments here without baths/showers and the people who live in them depend on public baths. It's inconvenient, but not discriminatory, in my opinion, for a gym or spa to refuse admittance since they are privately run businesses. A public gym, such as the Tokyo Metropolitan Gym, allows people with tattoos to use its facilities.
I definitely hide my tattoos from my Japanese family, landlords, clients, etc. On one hand, I've seen a surprising number of young people with neck tattoos here. On the other, I've noticed bar owners look uncomfortable when I took off my sweatshirt (and I'm nowhere near covered and I don't have Japanese-style tattoos). I think the stigma, however, also makes it more fun to have tattoos. I sometimes wonder if I would be as into tattoos if I still lived in Brooklyn, where more youngish people seem to be tattooed than not.