As least for nyc, there's no fare difference for nh between (7k base fare)
Nyc-tyo nonstop
Nyc-lax-tyo
So nh isn't charging more for the lax leg... Just charging a higher premium because u want to fly with them (or UA due to the JV) (and whatever reason the lax works better for your schedule)
nonstop UA/JL nyc-tyo charges 6-7k too
The 3k AC fare is actually 3 separate fare basis... NY-Canqda, canada-tyo, tyo-nyc. Think you got lucky , actual filed AC fare for nyc-tyo business is 6k