Actually I believe it is literally about "feeling small." If my memory serves me correctly Josh (along with his drug addiction) fought with anorexia; he was bulimic. From what I can tell, the song vents out the regret and guilt of his own "selfishness."
He's spent so much time and effort on becoming "thin" that he's missing out on the more important things in life. (I'm not sure how true this is to his personal life) but the protagonist of the song spent their own sister's wedding worrying about their image instead of enjoying the moment. And now that they've realized that there are more important things in life, it's too late (the sister is dying from cancer).
Through it all the sad fact remains that the mentality isn't gone, the protagonist still feels the need to lose weight.