U.S. retirement benefits normally need 40 quarters (10 years) of credits. If you split a career between the U.S. and Japan, you might fall short in each country alone. As long as you have at least 6 quarters of U.S. credits, the agreement lets you add your Japan credits to reach eligibility — the U.S. then pays a benefit pro-rated to your U.S. credits only.
A Certificate of Coverage is the document that proves you're exempt from one country's social security. For U.S. coverage, the employer requests it from the SSA Office of Earnings & International Operations. Japan's authority issues the equivalent when Japan covers you.
Under the U.S.–Japan agreement, a worker sent by a U.S. employer for 5 years or less normally stays under U.S. Social Security only and is exempt from Japan's system. Your employer obtains a U.S. Certificate of Coverage as proof. Beyond 5 years, coverage shifts to Japan.
Yes. If you have at least 6 quarters (about 1.5 years) of U.S. credits, the agreement lets you combine ("totalize") your U.S. and Japan credits to reach the 40-quarter (10-year) threshold for a pro-rated U.S. retirement benefit.
The agreement has been in force since 2005.
Pension taxation depends on Japan's domestic law and the separate U.S.–Japan income tax treaty (if any), not the totalization agreement. The totalization agreement only governs which country's social security system covers you and how credits combine. Confirm pension taxation with a cross-border tax advisor.