Exporting as fixed layout EPUB - Text spacing issues. Help needed!

Welcome to the world of EPUB standardization. (Well, no, since it doesn't exist.)

EPUB's one great flaw is that it is dependent on the viewer used, and there are very few that adhere to the actual EPUB standard. Calibre is one of the closest and my current preference for EPUB proofing; Thorium is the gold standard, almost 100% standard-compliant, but it has a persistent font-size bug right now that the developers can't seem to get around to fixing. But basically, if you have problems with the display on Calibre, you have (real) problems.

(For the record, Apple's viewer and Kindle Previewer are very good in their own ways, but both are quite nonstandard about many things and can't be relied on as a straight EPUB proofer.)

The problem is that fixed-page EPUB is a very binary format: it either works or it doesn't. If it doesn't, it's very hard to fix or tweak because of the complexity of how it writes and formats pages. My real recommendation would be to not use it, especially not for text books; it is suited only to "picture page" books like comics, graphic novels, children's books and the like. If what you have is all text or mostly text... reflowable is by far the better choice.

There just aren't many suggestions I can make in fixing the kind of problem you're seeing. With reflowable, you can write CSS style code that can modify and/or fix almost any export problem, but FXL is... all but inaccessible.

You could try the InDesign file fix: save your book file to IDML, then open that file and save it as INDD under a new mame. Export from that and see if the problems are fixed. (That process purges ID files of junk editing data, and rewrites the file structure, and thus fixes all kinds of faults based on small corrupted things.) If not... well, report back and we'll think of the next thing to try.

You do, by the way, have to have absolutely meticulous style definitions and application. You can't really have any spot or override or undefined or default style assignments in a doc intended for EPUB or Kindle. That kind of stuff will often print and export to PDF fine, but break in all kinds of ways with EPUB or HTML export.

You might find issues in this useful: https://nitrosyncretic.com/DPR/dpr_indesign_epub_basics.php

As for DRM, there's really only one accessible, workable solution: Kindle. Everything else is complicated and restricts how and where you can sell your book, to the point where whatever issues you have with Amazon/Kindle will be minor in the hassles of actually being able to reach your potential market.