The primary issue with the ePub workflow in InDesign is that it doesn't provide a real-time preview of the book while you work on it. While this is less of a concern when designing a fixed layout ePub, it becomes extremely frustrating when working on a reflowable ePub.
More worryingly, InDesign lacks a built-in validator, and we are completely dependent on a "exporting first, then validating workflow", which is completely backwards and incredibly inefficient. A built-in validator is a *must* when working on epub files.
The secondary issue is that the internal structure and code is completely hidden in InDesign. This means that custom code bits and pieces cannot easily be added, and require a rather awkward external CSS file approach. Not to mention that the underlying html code cannot be inspected easily or manually edited.
Worse, unless the author is very thoughtful about their content in InDesign, InDesign will inject useless containers with huge empty image files under circumstances. But these can only be identified after exporting the epub file manually in an editor, because InDesign does not expose these in any direct way.
The way InDesign creates interactive links (fixed layout epubs with page links for example) are non-standard and only work in Apple's readers. This can only be manually corrected after export again. Which is, of course, an upside-down approach, inefficient, and unreliable.
The third issue is that InDesign generally overcomplicates reflowable ePub layout. The GUI is less than forthcoming in this regard, because it never was intended for this type of ebook formatting in the first place. The overall ePub workflow is rather inconvenient, to say the least.
The fourth issue is that InDesign's ePub tools haven't really seen any major updates in a very long time. Rather than adding new features, some ebook publishing features have been removed along the way. (And Adobe seems to insist on restricting the web publishing to their own online cloud ecosystem only. Which means the author is required to invest in tools such as In5 to regain control over their own published html files.)
(...and I haven't even touched potential issues related to the workflow with images in InDesign and ePub files...)
Tools like Jutoh and Sigil (and even Calibre) allow for real-time previews while working on reflowable ePub books and offer built-in validation. The underlying code can be inspected and edited, if need be.
Which is the reason why I would suggest to work with Jutoh or Sigil if the author is considering a reflowable ePub.
Personally I moved away from InDesign and reflowable ePub publishing years ago, and I use both Jutoh and Sigil with a spot of Calibre for certain tasks. And as you've discovered yourself: Jutoh's export options and control over the export far exceeds those of InDesign (which can't even do proper HTML export!).
As for FXL ePub files: these are so fragile and unsupported on platforms like Windows, Linux, and Android - I moved away from them for the most part.
(Yes, Thorium Reader is an excellent FXL epub reader for Windows/Linux, but InDesign's non-standard linking is problematic and must be fixed manually after exporting the book from InDesign. And most users won't be willing to install a third-party reader anyway just to read one book...)
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