In the end it comes down to money. Many of the old homes are owned by old, lower-middle income earners. When a person dies, their descendants are taxed on their inheritance. In other words. If the owner of one of those quaint Tokyo homes dies, their kids will be taxed for their property on the extremely over-inflated land values of central Tokyo. The kind of money that no regular person earning even a moderate salary in Tokyo could ever afford.
Those families either have to give up their inheritance for a pittance, which is then snatched up by the greedy real-estate developers, bulldozed and turned into apartments for the rich, or to pay for the property, People are forced to take new loans on their property despite it being theirs, burying them in debt with no real hope for the future as salaries continue to spiral downward and Tokyo land values continue to shoot upward.
The government knows this. They could easily fix the law to support the people but as anyone following the Fukushima, Tsukiji Fish Market, Tokyo Olympic scandals can clearly see, Neither the Tokyo Metro, nor the Central Government gives two shits about the regular, hard-working members of society. They only care about enriching themselves and the giant companies owned by their friends and families, at the expense of the people they should be serving.
So while you're strolling the backstreets of Tokyo, lost in your fantasies, know that what you're seeing is likely not going to be there for long, and all the small, local, vibrant, individual parts of Tokyo that made the city what it was, are going extinct.
Photos from Iwamotocho (Between Akihabara and Kanda)