Totally give up trying to do you final ebook formatting in InDesign. Justification and paragraph indents are easily controlled by editing the ePub with an appropriate editor and tweaking the CSS rules.
You should accept that InDesign's ePub export will need final massaging in a real ePub editor. You will need to learn a bit of xHTML and CSS coding, though. I would recommend that you get both
Sigil and
Calibre. The latter is a bit of a "Swiss Army Knife" offering that is an ebook library manager will a good format conversion engine at its core. It includes a Reader app and a rather good Editor for both ePub and Amazon AZW3 formats. Sigil is a pure editor with some advantages over Calibre's Editor app.
Both are well supported and free. For support for either and for ebooks in general, I highly recommend you join the MobleRead community at
https://www.mobileread.com/