That is a dilemma. That’s the way InDesign works. It puts the footnote in the text box it is called out in. But there is a work around. I’m not sure how your Word file is set-up. Hopefully the Hebrew text immediately follows the regular text, and that the commentary follows the Hebrew.
Anyway–
1) You will have to use text frames on your master pages. I normally don’t use that feature, but it will be needed in this case. Have text frames on your master pages and then go to text frame options and select two-column, and plug in whatever your gutter size will be.
2) Set up a paragraph style for the first line/paragraphs of Hebrew so that it starts “next column.”
3) For your commentary text, set up your paragraphs to “span 2 columns.” If you have any heads in the commentary, those will also need the span 2 columns in those paragraph styles as well. Note: You can also add space above in those paragraph styles.
Basically, the entire job will be two-column, but not as two separate text boxes (and having to create a single one for the commentary. Instead, everything will be two-column, except where you specify that it is one column (which spans both columns).
I hope this made sense.
Dwayne
EDIT: Any word breaks that are wrong in my post are not typos. It seems that the site is breaking by line length. For example, I definitely have “Word” as one word, but when I see my post it is W at the end of the line, and “ord” starts the second.