This withholding mechanism is part of Japan's tax system. If you are not a Japanese tax resident, different withholding or reporting rules will apply to you.
How it works
In a "with withholding" specific account, whenever you realize a gain from selling stocks, the brokerage pays you the proceeds after deducting the equivalent amount of tax in advance. Tax is also generally deducted from dividends at the time of payment.
Benefits and things to watch for
Withholding reduces the burden of handling tax payments yourself each time. On the other hand, if you want to offset gains and losses across different accounts, you may need to file a tax return (see related page) — please confirm the details with a qualified tax accountant.