InDesign added the ability to annotate one or a few characters many versions ago. You might or might not get this to work for your situation.
So-called <i>furigana</i> are essential in CJK typesetting, but before CC versions the details were not available in the English-language interface. Adobe’s help file explains them here, using the alternate name, Ruby Text. You may still need to jump through some hoops to see the relevant menus in English, so you might want to experiment first with MS Word’s corresponding “Phonetic Guide” feature to get a general idea of how this works. Adobe’s Help says the offset of the ruby text can accept a negative value, which may or may not allow you to move the annotation below the parent text; MS Word apparently allows only positive values. Switching direction between RTL and LTR is obviously crucial for you but I don’t know where you can find out about this — ruby are seldom discussed on Adobe’s forums. MS Word limits the annotations to about 20 chars., another detail that could be important.
If you have some HTML experience you may already know that HTML5 can also handle ruby text. This is one of the more complex features added in HTML5 (and therefore ePub3), so you cannot assume it will work everywhere. Still, it might be worth checking out <i>Ruby Markup</i>.
I might experiment with single-line paragraphs, with alternating languages and directions, perhaps with tabs between words/phrases to tweak alignment. But that seems like a lot of hand-work.
Good Luck,
David