I can relate to your woes. This is a standard problem of codeshares! It does not depend on the alliance or airline. I've had the same for UA op by NH, IB op by AA, and also MH op by JL on exactly the same flight as yours.
I never was able to get the seats I wanted on that JL flight. HOWEVER on IB op by AA I had one of the Admiral's club lady put a "request" for preferred seats and ended up having exactly what I had asked for.
As a side info, ask for a seat on the left on the outbound (NRT-SAN) and on the right for the inbound (SAN-NRT) or in the middle. The 787 has terrible electronic window shades. On the outbound it may be OK because most of the flight has a sun fairly in front of the plane. On the way back however, the sun is on the left and you get a fair amount of light and a rather strong infrared heat coming through the window! I am not actively avoiding the 787 for that reason! JL has some funny "stick by friction, static electricity" shades, but most of the time, they don't hold....