If you assume that by going to the "Tools>Options>Display: Formatting" that you are going to change the look of all the emails that you receive, you are wrong.
If the emails you receive are composed with HTML coding, then it is up to the specs within that email as to how it will be seen. Your changing the Fonts or Size will not change those.
What will change are the plain text emails. Those are the ones that contain no formatting info within themselves, thus, at those times, your Thunderbird Options will take effect.
If a person is sending you an HTML formatted email, they have designed the look as to how they want you to view it. It would make little sense for your Thunderbird Options to override that.
I believe it may be possible that you could set Thunderbird so that no HTML messages come through as HTML, instead all you'll see would be is the plain text, and your Font settings would then take effect. But I am not going to bother researching this and telling you how when you are not too forthcoming and telling us what it is you are talking about, for you to explain your issue, even though many of us have been asking you for details.