How would they do it? Have a unique id for each envelope and enter citizen ID and ballot ID in a database as they hand you the envelope?

The process should be well known since all it takes to find out is go sit in an election committee.

That assumes that the Japanese version of democracy works similar to the ones we live in. Which it doesn't, at all. It's more of an authoritarian system with a friendly, democratic facade put in front when the US pressured Japan to modernize after WW2. A very interesting topic, I've recommended this book on HN before: Karel Van Wolferen - "The Enigma of Japanese power". Basically what we think of the system of modern Japan in the West are carefully doctored fairy-tales and mythology.

Can you be more specific what exactly my question assumes which is not true?

That 1. they have similar election committees and 2. anyone can go take part in them

How are they dissimilar to the western ones? Who participates in them? Can't the parties candidating in the election nominate their representatives into the committees?