Re entry Japan

Hi guys, I have looked through the internet and there are so many different answers/information that I just don't know what is correct and what is not anymore. Hope to find out more here.

I have to go back to my home country for personal reason and will be back again. My questions are about the quarantine rules when re entering Japan.
I understand that you have to submit a certificate of negative test result conducted within 72 hours prior to departing from the country/region where travelers stay when entering Japan. Here comes the part what confuses me/cant find the answer for.
1. Everyone that is coming back to Japan needs to quarantine for 14 days. Some information says that this can be done at home but other information I found says, first you need to quarantine for 3 days at specific facilities designated by the chief of the quarantine station undergo a PCR test on your 3rd day and if that test is negative. Your 14 day period of quarantine starts. Which on is it? 14 days only or 3 days + 14 days?
2. My second questions is about PCR test. I read that you need to take a PCR test upon arrival in Japan. And if the 3 day quarantine rule is true you have to take another test on your 3rd day?
3. Last questions and I couldn't find any information about this. Are the cost for:
- The PCR test on arrival
- Specific facilities designated by the chief of the quarantine station (accommodation cost for 3 days)
- PCR test on your last day of your 3 day quarantine
to be paid by yourself?

Thanks in advance

1: Depends where you are arriving from, and the particular rules that apply on that day. While the official notice on the MoFA page changes frequently, for the last month the changes have been small.
https://www.mofa.go.jp/ca/fna/page4e_001053.html
I know of someone that quarantined recently at the home of a family member (sister). However, for some countries it appears that there is are designated locations.
The guidance has been 14 days total. The wording could be clearer in section 3.i, but it is 14 days. (Occasionally they make wording changes to try to clarify things. You could check the Japanese version.)

2: You did not actually pose a question. Section 3.1 para 2 of the referenced web page (a few days ago it was section 2.1) says simply test on arrival and 14 days. But the section 3.1 applies for designated countries (and the long list).

3: AFAIK the tests on arrival are not charged for. The 3-day test, not sure. As for the cost of the facility, that depends on which one you are at.

If in doubt, call MoFA/Immigration. on the page https://www.mofa.go.jp/ca/cp/page22e_000925.html there is a contact given for "procedures upon arrival at the airport" and for "quarantine measures such as staying at home or a place designated by the Chief of the Quarantine Station".
Also: https://www.mhlw.go.jp/stf/seisakunitsuite/bunya/kenkou_iryou/covid19_...