I just realized that the Identity Chooser add-on is what is making the background color yellow. Fortunately, I can change the background colors under Tools > Add-on Options. That neatly solves the problem.

re :When composing messages with the dark theme, the font for to/ from addresses and subject is white but the background color is yellow.

You must have something else doing this, maybe an addon. I've got some old userChrome.css file that is currently effecting my dark theme, so need to get it sorted. But, when I select dark theme and restart with Addons disabled to give me default. The dark theme has a dark background in all FROM TO SUBJECT areas and uses white font. There is no 'yellow', this is a dark theme.

Suggest you restart in Thunderbird Safe Mode to see if you get an all dark result with white text. https://support.mozilla.org/en-US/kb/safe-mode-thunderbird

If yes: Try disabling addons one at a time (and restarting Tb) to see which one is effecting your view.

Do you use a 'userChrome.css' file ? If yes, then you may have a setting that is causing the issue.