This is wrong on so many levels that I created an account just to answer.
1. In big cities, where most of the Japanese population lives, space is scarce. Recycling rules are strict, meaning that you cannot take out the trash when you want, and have to store them somewhere in your home. Bigger "trash" need to be recycled, you have to pay for the service, and it can take months (happened to me) until they come to pick them up (so in the meanwhile, they have to go somewhere). Read this here for a longer answer: https://www.quora.com/Why-do-Japanese-homes-tend-to-look-a-bit-messy-while-Japanese-people-usually-pay-a-lot-of-attention-on-their-outwards-apparel-clothes
2. "a bath and a toilet are placed in different rooms" only if you live in a house, or have enough money to live in a big enough flat. Many people have what they call "unit bath", which is a frefab unit containing both bathtub, toilets and a sink. Read this: https://www.apartmenttherapy.com/at-asia-yunitto-35316
3. Again, the majority of the population live in cities. The contact with nature is mostly found on the patterns printed on the cans of beer (sakura for spring, momiji for autumn etc.). There are many parks though, and they are usually open 24h/24.
4. Mmmm... maybe.
5. See point 1. Not everyone in Japan is KonMari :) (although you might want to read her book if you like this approach).
I live in a house in Japan that was built in the early 1980s. The shower and bath are in one room, the sink in another, and the toilet in yet another room. The washing machine is in the sink room, which is next to the bath, and is set up so that hot water from the bath tub (which is clean since soaping is done outside the tub) can be pumped into the washing machine using a special attachment.
I have also rented various small apartments (1K or 1DK) in Japan and most of them came with a bath in one room and toilet in another. The bath and toilet were never in the same room. One old apartment did not have bathing facilities, so I had to use a public bath.
1. In big cities, where most of the Japanese population lives, space is scarce. Recycling rules are strict, meaning that you cannot take out the trash when you want, and have to store them somewhere in your home. Bigger "trash" need to be recycled, you have to pay for the service, and it can take months (happened to me) until they come to pick them up (so in the meanwhile, they have to go somewhere). Read this here for a longer answer: https://www.quora.com/Why-do-Japanese-homes-tend-to-look-a-bit-messy-while-Japanese-people-usually-pay-a-lot-of-attention-on-their-outwards-apparel-clothes
2. "a bath and a toilet are placed in different rooms" only if you live in a house, or have enough money to live in a big enough flat. Many people have what they call "unit bath", which is a frefab unit containing both bathtub, toilets and a sink. Read this: https://www.apartmenttherapy.com/at-asia-yunitto-35316
3. Again, the majority of the population live in cities. The contact with nature is mostly found on the patterns printed on the cans of beer (sakura for spring, momiji for autumn etc.). There are many parks though, and they are usually open 24h/24.
4. Mmmm... maybe.
5. See point 1. Not everyone in Japan is KonMari :) (although you might want to read her book if you like this approach).
I have also rented various small apartments (1K or 1DK) in Japan and most of them came with a bath in one room and toilet in another. The bath and toilet were never in the same room. One old apartment did not have bathing facilities, so I had to use a public bath.