Concerning dark mode issues, I haven't had a chance to look too much. Maybe it is only tables with alternate row styling, e.g. editing TOC and the Plugin list in preferences.
The only possible relevant issue I could find:
QTBUG-80757: QTableWidget Palette Returns Wrong Alternate Row Color
https://bugreports.qt.io/browse/QTBUG-80757
Then there was at least one other about native styles though I didn't read it too much. Maybe it is related to SigilDarkStyle? I didn't look to see where it is called. Maybe with creation of each EPUB document? Seems in such cases, maybe sigil dark mode is set. For instance with each, it seems the table styling is incorrect, yet after I toggle dark mode, I think it retains the correct style. I haven't tested much but that seems to be the behavior. Perhaps with Qt6, you could sometime experiment with using the native style w/o changes and perhaps that enough might work?