In 10.3.x, however, I discovered a way around this. In the Input Menu configuration panel (under International in System Preferences), activate Kotoeri (the Japanese input method) and select Romaji. While Romaji was meant to allow Japanese to be written phonetically using western (i.e. Roman) alphabets, there is no reason you cannot use it for your day-to-day needs as an English speaker, for example. Selecting Romaji in the Input Menu replaces the flag with a non-presumptuous capital A icon, and you can configure it to work with various keyboard layouts, though the default is US.

