Colors and erasure of color assignments

I've never found a way in the GUI to set the background color.

You can select the messages you want to unset and run this AppleScript in Script Editor:

tell application "Mail"
	repeat with aMessage in selection as list
		set background color of aMessage to none
	end repeat
end tell

It's probably the same as it was in Ventura: Control (right) - click on the email and in the dropdown contextual menu click on the flag that has the box around it to remove it.