Please note Keyobard layout and Input Method are seperated. Keyboard layout should follow your physical keyboard. Then add the required Input Method.
Also, for the Japanese keyboard layout found in eOS. I found no way to do transform and only Katakana can be inputted.
For adding Input Method, please follow these steps.
System Settings > Keyboard
Go to system settings, then "language & region" and use the "plus symbol" in the lower left of the window to add Japanese as an language. Set region and format as you like. These steps might be optional, I didn't try.
Then click to keyboard settings (lower most left big button). Again click the "plus symbol" on the lower left and search for japanese. ...
There are two ways you can change the language setting:
change Keyboard Which you can change by Alt+Shift
change input method Which you can change by Alt+Space(By default disabled)
Option one is easy even you can change at login-screen, But if you changed input-method this you can't change at login-screen using Alt+Space because ibus is not running by ...