There are many qualifying questions that would affect the answers:
Q1. What is your nationality?
Q2. You say you're on a Spouse Visa?
Q3. Do you have any Overseas Income; Capital Gains, Dividends, Rental Income, Pension(s)
Q4. How long have you been in Japan?
If you are on a Spouse Visa, then You are a Resident for Tax Purposes.
If you have been here for less than a total of 5 years (5 x 365 days) in the last 10 years, then You are a Non-Permanent Resident (NPR) for Tax Purposes.
If you have been here for more than a total of 5 years (5 x 365 days) in the last 10 years, then You are a Permanent Resident (PR) for Tax Purposes.
You should see a qualified Tax Advisor
You can start by reading the Annual INCOME TAX AND SPECIAL INCOME TAX FOR RECONSTRUCTION GUIDE
https://www.nta.go.jp/english/taxes/ind ... /index.htm
Currently, the 2020 Guide (last year's) is still posted, but the 2021 Guide should be posted in Jan/Feb 2022, just in time (I would argue too late for) 2021 Filing in March 2022.
https://www.nta.go.jp/english/taxes/ind ... x_2020.htm
A1. Your iDECO and NISA providers will supply End-of-Year reports with the numbers you need to file.
However, will your new employer provide a 401k? If so, this may affect the amount you can contribute to the iDECO.
You would provide these numbers to your employer and they would normally be handled under the Nenmatsu Chousei.
A2. In the Tokutei account, they will handle the tax through withholding, and the reporting for you. As you are only buying at this time, there is nothing to report.
When you sell, they will handle the tax through withholding, and the reporting for you. You Only need to file if your total income/gains other than your Employment Salary exceeds Y200,000. Then you have to file, but you get the credit for the Tax withheld.
Any gains outside the Tokutei account, or if you are PR, outside Japan (whether you remit the funds to Japan or not), that have not been subjected to Japanese Tax Withholding will have to be reported over Y0.
A3. If PR, any and all income/gain outside Japan (whether you remit the funds to Japan or not) is subject to Japanese Taxes, and you have to file.
If NPR, certain types of income/gain outside Japan (whether you remit the funds to Japan or not) may be subject to Japanese Taxes, and you have to file, but other Foreign Sourced Income (as defined by Cabinet) is not subject to Japanese Taxes unless you remit the funds to Japan, when the Income or Capital Gain portion becomes subject to Japanese Taxes, but not the whole amount.
Your Hypothetical govt. bond or international stock: Only any Interest, Dividends, and Capital Gain are taxable, not the amount you paid to acquire them or the expenses incurred to buy/sell/hold the securities.
Gifts: In any Tax year you can receive Gifts tax free up to a Total of Y1,100,000.
If PR, and If your total received gifts exceed this amount, you would have to file and pay Gift Taxes on the amount exceeding Y1,100,000.
If NPR, Only gifts received in Japan and gifts remitted to Japan are subject to Japanese taxes, and you would have to file and pay Gift Taxes on the amount exceeding Y1,100,000.
Inheritence is too complicated... there are other threads where Inheritence tax has been discussed, or you could start a new thread with any specific details...
You can claim Foreign Tax Credits against the Japanese Taxes for any taxes paid overseas on any overseas income.
You can also consider Furusato Nouzei as a Tax reduction strategy, if you have not already.
