Dual-nationality use

Hello,

My son is Japanese/British, holds a British passport and resides in the UK. I understand this makes him eligible for a JR Pass. When we arrive in Japan, will it be OK for him to enter on his Japanese passport, and then for him to show his British passport when we exchange for the pass? My concern is that his British passport will not show the tourist stamp inside, and the JR office will refuse to exchange for the pass.

If this is a problem he can enter on the British passport.

Thanks