I'm assuming that "short-term rental" means your standard "night or two" hotel rooms (not just extended say). It sounds like it, from the report. I remember staying in hotels in Japan, and they would say 1,600 Yen per night, and ... I get the bill for two nights, and it's 3,200 Yen. Not so, US hotels.
I haven't stayed at a 1600 yen capsule hotel before, but my favorite one-step-above (small private rooms, shared bathrooms on each floor) hostel-lite, which is usually two to three times that amount (when they have availability, I think too many other people discovered it), started charging like a 100 yen towel exchange fee if you wanted a fresh towel during your stay. Then at bigger hotels you start getting into extra taxes (a few hundred yen per night) when your rate exceeds 10,000 yen. Especially when your rate fluctuates over a stay, it's just a weird small amount of extra hassle you have to pay when you check in separately from the online system, though the systems do usually mention somewhere that there might be additional tax related fees when you arrive. Still, it all feels pretty smooth vs. US hotels where if they include for example any snacks in the room or drinks in the fridge you don't even want to touch them for fear of a surprise $20+ charge later. (A work friend did successfully win against a hotel that tried to charge him drink fees; their "smart" fridge detected he removed some drinks from the fridge to make room for his stuff, it did not detect that he put them back, and these weren't the kind of drinks that would spoil if left out.)