Maybe you should try using "theWord" Bible program. There is full documentation on making the different module types. It does support notes in the Bible view. (as popup or inline/end of verse or chapter with markers)
Another bonus of going this route is that there is an android app called "MySword" that can migrate theWord files to its format, and footnotes in the Bible view are supported there.
I'll take a look at theWord. Is there also an iOS version? I would like to go mobile with this eventually.
BTW, I did get my own example dctx and cmtx modules working so thank you all for your jumpstarting!
What controls the existance of the deuterocanonical books and their font color in the BibleBook list (for example, Latin Vulgate)?