As I said, engineering food isn't bad in itself, it depends on what goals you have when you engineer it. Just because Japanese people eat a lot of engineered food doesn't mean it is bad for them if that food wasn't engineered to make them fat.
Many say they slim down as they visit Japan, so I wouldn't rule it out.
What I'd want to see is if two countries that has the same snacks available had vastly different outcomes. But as far as I know most countries has domestic snacks so it varies wildly around the world. For example, why is Czechia much fatter than Slovakia? They were the same country 30 years ago.
I'm sure Japan has a variety of unhealthy foods, I don't see how that matters. That unhealthy food exists in Japan doesn't tell us anything about how much of it people actually eat.
That's why I linked the video, its author talks about the experience of the average person, here's an exact link: https://youtu.be/lr4MmmWQtZM?t=176.
I cannot stress this enough, the only thing that matters is what is readily available to the average person. That's the determining factor of most people's diets, not what's theoretically possible to purchase.