1. JAL C gives 3 x 32kg checked baggage allowances and 2 x 23kg in Y on all international flights.
2. MSC rules apply to single ticket. Since you are issuing 2 different tickets, when you check in at HKG with CX, you are only entitled to 20kg and will most likely be charged extra baggage fee.

you should have issued HND-HKG on JAL instead. At least you will get 2x23kg that way