It's better to start with format & styles for ebook and then edit a copy for paper/PDF when the content is proofed. InDesign is old style DTP for paper and now even for paper/pdf few books need it. Publishers use it out of inertia.
Ebook source should have none of what paper / PDF needs:
- Page registration
- A defined page size (for editing for ebook just pick all pages A5 or similar)
- Multiple page styles, each with own header/footer. Left & right versions. First page of chapter, front matter, title page, contents, rear matter, body left & right etc
- Line height (evil in ebook)
- Hyphenation is WYSIWYG
- Page numbering
Things with poor or zero ebook compatibility, trivial for paper:
- Text flowing round objects
- Drop caps
- Fractional spaces (digits & units)
- Small Caps
- Images inline as if text (fails when font resized)
- Tables
- Multiple columns
- Special aligned content (table or column)
- Content across or aligned on two pages side by side
- Landscape.