For my free novels which I deliberately keep the styles to header2 and body text, it is surprising the amount of crud that all the ePub conversion softwares generate, especially since they are just zipped web-pages.

These days I usually get 90% of the way on google docs, then do the final editing on LibreOffice which can add things like tables of contents and cover image, if it opens on Kindle, Kobo and Calibre I consider it job done.