This is just about the unwisest thing I have ever heard. As someone who has lived in Japan for 5 years and married to a Japanese, my advice to you is NEVER ASK JAPANESE FOR AN ADVICE! Japanese staff are not taught and trained to be flexible, in fact, they are not even trained to think independently. Everything goes by the book and nobody can question the SOP. In your case, you asked about the middle name question to a Japanese, since Japanese are not familiar with middle names, they will follow what their training manual says, which is ticketed name(s) must match the name on the passport.

Next time, enter your middle name after your first name WITHOUT A SPACE. For example, JIMDANIEL or MICHELLEANNA etc. I have done this hundred of times and never ran into a problem. And don't ask a Japanese again for advice.