Re diet: putting aside that alcohol-per-capita consumption here in Japan is less than the OECD average [1], and also how the article is actually about how the introduction of meat into the Japanese diet has caused a decrease in strokes (i.e. this is probably off-topic); it is true that if you are eating out cheaply, you'll likely find lots of rice and meat stuff like gyuudon (beef on rice), katsudon (breaded meat on rice) and what not.
But a normal Japanese meal generally has a pretty good mix of stuff - some fermented side dishes (tsukemono), some veggies, miso soup, some rice or noodles, some fish, maybe some meat. Perhaps my wife is an outlier, but every meal she's cooked for our household has had at least 3 dishes of different categories as a part of it, and my impression from seeing other households and just looking at a typical bento box, is that that's a pretty normal expectation for any healthy meal. Someone else pointed me to this Youtube video on the topic on a different thread, and I'd say it's pretty accurate [2].
When I go to drinking bars, izakayas, with Japanese people they usually tend to do the same and order a variety of small dishes too - it's not common to just get fried chicken (karaage), but rather people almost always also throw in salty drinking foods (otsumami), which usually include seafood, pickles and vegetables (shiokara, takowasa, various tsukemono and so on). Even then, if someone orders sweets or something, they tend to be a lot less unhealthy than American counterparts (use of less calorific ingredients like adzuki beans or black sesame, compared to a cheesecake or something; and if you did order that cheesecake, it'll be 1/4 the size of what you got at the Cheesecake Factory, and be a whole lot less sweet and rich, as you've pointed out).
It's not straightforward to get a really authentic food experience if you're coming as a tourist who doesn't know locals nor the local food scene well. My first impression was also that it's a ton of rice and meat, but after living here it turns out that that is the case... if you think that Japanese food is all sushi and ramen, and are being sold food to satisfy a standard American tourist, who thinks that anything pickled is gross, anything served cold besides ice cream is disgusting, and that a meal that doesn't include a giant hunk of meat, isn't a meal at all. Get past that, and you'll find that most Japanese people don't eat like that at all.
So yeah, I think diet probably does make a significant difference, as you can tell plainly by how few obese people there are in Japan; and recently the government finally seems to be doing things to reduce tobacco consumption (you can't smoke in most bars and restaurants in Tokyo anymore, when you can it's generally e-cigarettes only, fueling a huge shift to IQOS/other brands e-cigs which have as of 2019 taken over around 16% of the tobacco market [3]; anecdotally it feels like a lot more than that as of 2021 living here).
Re culture: Agreed, here in Japan (and in other parts of Asia too) it's pretty normal for friends to tell you things like, "wow, you got fatter since we last met!" to someone who's much less than 26 on the BMI index. It's not really considered insulting like it is in the West. That said, female Japanese models tend to be insanely skinny, creating an unrealistic concept of beauty - but that's hardly unique to Japan.
[1] https://www.who.int/substance_abuse/publications/global_alco...
[2] https://www.youtube.com/watch?v=lr4MmmWQtZM
[3] https://apps.who.int/tobacco/publications/prod_regulation/ht...