> If you live and work in Edogawa City, or Katsushika, or Nerima
I only used the data I found in the referenced article. I used the "budget" option that is "located outiside central Tokyo and about a 30- to 45-min train ride to a major Tokyo station." Edogawa city is even closer than that estimation (about 25minutes to Toyko station and less than 20 minutes to a major station). So if the numbers in the article are correct, the 45000en example I cited would be more fitting to something like Funabashi. For the places you mentioned the article claims 70000en/20m², so 3500en instead of 3000en per m².
You might be correct though that you have less reason in Tokyo to go to the city center compared to a German city, e.g. for work, entertainment and night-live.
Edit: Your abandoned houses example is very interesting though. I also had the feeling owning property a bit outside of the centers isn't that hard/expensive here. Especially as the houses are rather simple wood constructions.
> And I haven't seen the variety and prices eating out anywhere else either. See if you can get a salaryman to take you around on a tour of not-so-secret 500en per meal shops.
Oh yes. Food prices were one of the most surprising differences for me. Eating out can be surprisingly cheap in Japan (e.g. at these 500en shops or supermarket excellent bento area). It's amazing. In fact I haven't cooked a single time for myself while being here. On the other hand, prices in supermarkets are way more expensive than in Germany. I pay 50% to 100% extra compared to prices at Aldi or Lidl in Germany. Especially fruits (and anything fruit related), Jogurt (granted, not really a domestic product), bottled water and drinks in general. Even rice is about 100% more expensive (about 120en/kg for the cheap one in German supermarkets)!
This results in the funny situation that for me eating out at cheap shops in Japan is maybe 20-30% more expensive than cooking for myself, while in Germany eating out at cheap shops is 2 to 4 times more expensive than cooking for myself. In the end I can manage with ~900en per day in Germany, but have to cook myself 6 times a week, while I spend 1500en per day in Japan and eat out 7 days a week.
Edit2: Eating out foreign food in Japan (e.g. pizza) is extremely expensive though. While eating international cousine in Germany (including a lot of available Japanese sushi and Ramen restaurants) has absolutely no price difference to the domestic restaurants. Actually Chinese, Italian and Burgers are regularly cheaper than German restaurants.
Edit3: Bottled water is also an interesting one. The cheapest bottled water in Japan is about 8 times more expensive than the cheapest one in Germany. Yes the tap water has a good quality and is drinkable, but I'm a "water snob" and can't stand even a slight taste of chlorine and some other usual suspects. The only tap water I found acceptable was in Nagano.
That's what I mean with some countries being better in one area, while the others are better in another area. It's not that easily comparable and your expectations in another country are heavily influenced from what you are used at your home country.