How do I best navigate the family name issue for a child with a Japanese mum and European dad?

My baby was born in Germany and has my last name on her birth certificate. My Japanese wife kept her name when we got married so we have to register the baby under her family name in Japan. When getting the passport I guess we can get my foreign name in parenthesis if I understand correctly, but does anyone have experience with this and will it cause lots of problems down the line?