Typing macron using the Kotoeri Romaji mode
While reading your question, I happened to stumble upon the (imho) easiest option:

Simply uncheck the "Romaji" checkbox under Input modes in your Japanese/Kotoeri pane in the System Preferences. Then you can choose an easy keyboard shortcut for switching exclusively between U.S.Extended (with the āēīōū capability) and the Hiragana Japanese mode.

Since I use a Japanese Apple Keyboard which includes the 英数 (Romaji) and かな (Kana) keys next to the space bar, this is ideal for me, but you could just use any other shortcut as well.