Yeah, it's kind of a gray area...I know for sure Emirates/Cathay, etc. have zero obligation to honor USERRA....
Is this contract structured such that you're employed by crew (I would define this as crew's name is on your paycheck)??? And is crew paying you offshore or from a us account? If so, I would say they are required to abide by USERRA and allow mil leave.
If the contract is a direct employment with the Japanese owners, they have zero obligation to let anyone go offshore for mil leave.
Interestingly, I think we might have just discovered one of the reasons they weren't allowing mil time--crew would be in a sticky situation if someone had to leave for extended guard/rsv duty, because as a US co. they would have to honor that person's absence, yet Air Japan might not be happy about taking back a pilot who suddenly had to leave for 3 months...crew would be stuck between the desires of their client airline and US Federal law...