@Kovid,
I'm not sure whether you're still following this thread, but if so, I found a couple of other GUI things which are invisible in nightmode on Win10:
- the vertical Separator lines between tool buttons in toolbars of both main calibre GUI and Editor.
- the optional gridlines (set in Prefs>Look&Feel) in the main calibre library window. They're only visible on rows which are currently highlighted.
I like nightmode a lot.