Visa will expired during application process?

Hello, i plan a trip though japan and want to stay 3,5 months, so i have to get extenison. The onlly time i will stay for a longer time on one place ist the last month of my trip (between month 2,5-3,5). That�Ls the only time i can go to an immigration office. Now is the question if it�Ls ok, when my 90 day�Ls visum expired during the workingproces for the extension because it will expired 2 weeks after i will submit the application of extension. And i read things like it can last 4 week or 3 months(?!).
Many Greeting :))

When you apply for your extension, you get the usual permission to stay for an additional 2 months after the expiration of your current period of stay or until a decision is made.

First what is the reason for your extension?
There need to be a valid reason for that.

Only 7 countries are applicable to extend the temporary visa.
those countries are Ireland, UK, Austria, Switzerland, Germany, Mexico, Liechtenstein

Citizen from those countries must apply for an extension of period of stay at a local immigration office before the expiry date. Indeed application can take two to 3 months. It takes as long as it need to take.

Maybe a short trip to Korea and back would also be an option.