This guy gets it, mostly.
Saying Japan is ultra-conformist is buying into clickbait. There are always exceptions to the rules, and the exceptions are more common than the conformists. Of course, if you are an employee at a super Japanese firm, you gotta look and play the part. If your kid goes to a prestigious, competitive high school they gotta wear the uniform and follow the rules. Not too different from most places, really. There are punk rock weirdos, fashion weirdos, mortorcycle hooligans, drag queens, dirty gross old men, loud teens, slackers, hipsters — and yes, even anime losers. There are people who eat on the train, even though "you're not supposed to;" eat or talk in the phone while walking, even though you're "not supposed to;" make a fuckton of noise and walk outside their house in their boxers even though "it's rude," (I've seen it) and so on. If you draw incessant attention to yourself, disturb others or act like a fool, you'll get rightfully called out on it. It's mostly butthurt fat weebs and MUH GENDER types with Danger Hair who turn everything into a crusade. If you laugh off the stares, speak the language and act relatively sane, you'll get by.
As to restaurants and stores banning foreigners, it's a load of bullshit that was perpetuated by some loser American who obtained Japanese citizenship, then changed his name to a Japanese one to prove a point...and ended up being unable to find any solid proof of discrimination aside from a bathhouse in rural northern Hokkaido that banned foreigners because Russian fishermen would come in completely sloshed and trash the place — meaning they couldn't follow the rules. (That American-turned-Japanese eventually got dumped by his Japanese wife and fucked off back to America, so he has an obvious bone to pick against Japan. Unreliable narrator with an agenda.)
The only place I've been turned away from was a bar that turned out to be members only. Anyone who cries DISCRIMINATION is usually unable to understand the nuance of "we don't speak English, so we are afraid we won't be able to help you."