For what it may be worth, I read mostly ePub since I prefer the font rendering. The only time I've seen black on black using Dark Mode is when some moron specified the text color as black. If you care to, you can use either Sigil or calibre's ebook-editor to look for any of the following in the ePub (text/HTML or CSS stylesheets):
Code:
color: #000000;
color: black;
color: rgb(0,0,0)
and remove them.