There would certainly have been training flights for the crews on the 787, the question is if they were with or without passengers. ANA did their A380 training flights without passengers, whereas we often see European and US airlines do short-haul flights with passengers. JAL does indeed have crews that can operate the A350s, and could use the domestic flights to expand that base, but I would guess the cabin crew would need some getting used to the new cabin as well.

If JAL wants to keep the new cabins under wrap until the last possible moment for the New York debut, we would probably not see domestic flights.