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I came across a hopelessly lost Thai lady at a cafe trying to find her booked apartment the other day, who did not receive full details of the address of the apartment. Upon calling, the host with strong Chinese accent kept on directing us to a location in Arakawa ward, which was a communal housing run by the municipal government intended for people with low income under the social welfare system (it has been repeatedly reported that such housing is rent out illegally by foreign - some or perhaps mostly Chinese - hosts to apartment rentals in major cities such as Sapporo and Tokyo). The original booking was actually two rooms in Asakusa, Taito Ward, and only after several telephone calls the guy understood his error.
It really is disturbing local people, including I as a resident who had to endure stupid foreigners at my apartment building barking out loud in the night and leaving inappropriately mixed trash at wrong dates. These stupid people buy new suitcases and leave the old unwanted ones on the street and think it's completely acceptable. If this is all done on personal basis among friends I would forego, they seem to think it's a new systematic business competing with proper hotels and existing apartment rentals which have to comply to laws and standards plus pay appropriate tax.
You are far better off to be staying in a hotel in Japan, especially if you are a first timer. Not only is there a standard of hospitality available (look at reviews) but there is staff available from whom to get advice and help.
Bag the Airbnb in Japan, and go with hotels,
So to answer directly to your question without my subjective views. Q: Are Airbnbs legitimate? Are they safe to rent? A: Some might be.
Not sure that I really understand your problem.
The new laws have caused some confusion, but as time goes by the legitimate hosts have received their licences.
If you book through Airbnb then they will only let you book with a fully licenced Airbnb host.
I booked accommodation for my next Japan trip almost a year ahead and Airbnb cancelled two bookings as it became clear the hosts were not in possession of the licence.
Airbnb returned my money AND gave me compensation for the inconvenience. I then had the choice of rebooking a different Airbnb where the host was now licenced, or I could make alternative arrangements if I chose.
I thought this was very decent as they could have simply given me a credit note - so I would say, trust Airbnb and book through them.
p.s. this is my fourth trip to Japan, I am an elderly single woman traveller and have never had a bad experience with Airbnb, even before the new legislation kicked in.
There is no comparison with a hotel. Hotels are lovely but you will miss out on many aspects of Japan. I cook, shop in the local markets and stores, stay in residential areas, wander the backstreets, and explore the nooks and crannies ... so seeing the Japan that most tourists don't.
(and of course I do visit the famous places too!)
Hope this helps!