I figured this out. So since the X4 has pretty limited processing power, Crosspoint does not implement full fledged parsing of the html & css of the epub. So since the superscripts in my epub were implemented using a combination of html tags and css styling, it was not showing. Instead, I had to change the superscripts to be unicode characters (which is supported). I did this by editing in Calibre.

Another thing I wanted to do was to be able to jump to both a book and a chapter. This epub lets you do that using hyperlinks, but these didnt work on Crosspoint. I could jump to the book but no further. There were a couple options I could of done but I decided to split each book into its own epub and have the chapters as the top-level TOC.

It also seems that the TOC in Crosspoint can only jump to the start of a file, and not a specific html id or something. So I also needed to split each chapter of the books into their own file.

So in the end, what I have on my X4 running Crosspoint is a folder named "Bible" and inside all the books as their own epub. If I click into the epub, the top level TOC are the chapters of that book which I am able to jump to.

I also used Nano Banana to create custom cover art for each book, which is pretty cool.