The Tokyo layer has an empty extent. There was an issue with handling those--it's been fixed at 10.5.0, so you now get a list of transformations.
Tokyo_1 layer gets a different sort order of transformation due to adding new transformations. The top entry, Tokyo_to_WGS_1984_NTv2, is the same on both lists, which is the one that generally should be chosen. In 10.5.0, there's a different list of transformations because we added the JGD2011 grid file.
Tokyo_2 layer has an extent that is outside of the range we use for Japan. The easternmost longitude is 120 E so no transformations are found. That's an improvement over 10.3.1 behavior.