She is trying to motivate people at home to get into a work mode rather than "lay around the house" mode. She feels that by getting dressed and putting on shoes, your mind is affirming "now we are ready to get down to work." She isn't into natural health.... YET!
I get the concept of "Now we're getting organized and ready to start the day by getting dressed." But since I don't wear shoes I translate it into changing out of my pajamas and into my bathing suit or exercise clothes. THEN I'm ready to start my day.
Flylady is a good resource for people who need some help getting organized. But I wouldn't take health advice from her.