> Japan has a serious problem with lack of sound proofing in most of the buildings you'll come across
In older or cheaper buildings this is true. However if you pay you can have better sound proofing. For example some Japanese mansions (residential low-rise condominiums) are built from reinforced concrete and isolate sound fairly well. You just have to be careful to read about the building and its construction. You also have to be willing to pay extra for better construction materials.
> as well as some discrimination (not necessarily racism) you might find while looking for housing
This is true for rentals. I also want to clarify Japanese also experience discrimination so it is not purely a non-Japanese thing. Generally landlords have freedom to put whatever restrictions they want on who they rent the unit to. But this is for good reason. A landlord cannot easily evict a tenant. So the landlord is taking a huge risk in trusting that the tenant will respect the contract and actually pay the rent.
I will say in buildings owned by corporations or businesses, they sometimes don't have any discrimination by nationality. They do tend to have higher requirements for income and may discriminate based on your current company employment contract. Also they may require a specific guarantor company which tends to be more expensive. The guarantor company is sort of a risk insurance for the landlord paid by the tenant.
However things are quite different if you buy the land outright. Here the only restriction is bank loans. If you do not have permanent residence, the number of banks willing to lend money are very few. If you have permanent residence then you have many more banks to choose from. Otherwise there is no restriction on who can buy land.
> Unless you have a company dealing with this stuff for you, you're going to have some headaches.
I think it is all about perspective and expectations. In Japan the Japanese are used to dealing with bureaucracy (though many Japanese also really dislike it). The information is readily available, you just have research yourself. Otherwise you have to accept that you are moving to a non-English speaking country and it is your responsibility to find a way to understand the local language or get someone to help you.
I do agree that there are still many headaches to adjust to Japanese business and culture. But I also don't understand why everyone has an expectation that Japan must change to meet their expectations. Japan is a first world country with many issues, but it isn't a place where you can expect to be free of first-world problems.
For example in the US nearly nobody bothers to complain about credit rating agencies. Maintaining your credit is seen as something you control. Which isn't necessarily true. Credit ratings greatly affect American lives. So everyone is in a way obligated to participate in a non-government created scheme yet nobody bats an eye. Just sign up for a credit card.