This is inaccurate.
The font settings under Mail > Preferences: Fonts & Colors effect only the "classic" (i.e., ancient, inefficient, ugly) layout available under Mail > Preferences: Viewing. Without the "classic" layout enabled, the font/size interface does nothing at all. You can click at it until carpal tunnel sets in and absolutely nothing will change.
This has been the case since the new layout was introduced - was it one or two year's ago? Mistakes happen, but must they go on for years? A quick web search shows about a quarter of a million hits, ranging from baffled to plaintive to furious, and yet nothing has ever been done about the problem.
There's a unique quality of frustration that occurs when faced with the profound ontological uselessness of dysfunctional software. It resembles having one's car replaced with the dashboard mockup they install on kid's strollers to keep them distracted, but has precisely the opposite effect.