Thanks so much for the replies here.

I was definitely sure he would need to enter and leave on his German passport. My only concern was that the SFO-HND was booked under his old passport, so the booking includes an extra surname. Didn't want to get to Checkin and JAL team say "no go". His photos and DOB and everything are identical.

Sounds like we should be OK just to turn up to check-in with both passports and show just the German one at immigration. I know he MUST leave/enter Mexico with his Mexican one by law.

Appreciate the input