When you hover over the background, you get help text that says "Hold ⌘ to set fonts individually." But when you hover over the theme elements in font mode, it very much implies that you'll be changing only that element. I almost posted a bug report before I saw the generic help text.
Possible solutions:
Include "Hold ⌘" prompt in all help text, not only when the mouse cursor isn't hovering over a text element
Change help text when hovering over text element to say "All fonts", and only name the element (e.g. "Result Subtext Font") when actually holding ⌘