As to the statement: "All new buildings in Japan are now pretty much impervious to earthquakes". No not by a very wide margin is this true..
Let me clarify this as I was trying to be responsive to the OP's question specifically regarding safety...... Absent flagrant and criminal violation of the building codes, there are no earthquake related life safety issues with any buildings being built in Japan.
Also I would stick to my earlier statement that economics depend on individual circumstances and specific properties. Personally I'm long and also bullish on central Tokyo, but I think even for central Tokyo you need to take into account other factors including: can the buyer get financing or do they need to pay cash, can the buyer absorb a large short term hit if there is a cyclical downturn, with a brand new building is the buyer willing to accept the above market premium for newly built buildings, what happens if long term trends change, with a premium property can the owner wait a year or more if they need to sell, what's the real opportunity cost of capital (not limiting yourself unrealistically to yen assets.)