I'm a fellow Writing Excuses lover. I discovered their podcast somewhere during Season 11 and then decided to backtrack and listen to everything that came before. I've listened to literally hundreds of episodes, probably averaging 4 a week for the last couple of years.
I've found so much good advice, and I believe it's an incredible resource. But they are shy on certain kinds of content.
Their strength: the mechanics of writing.
Their weakness: writing books with meaning.
Writing Excuses can teach you a lot about how to craft a plot, fill it with interesting characters, interweave subplots, convey emotions, create suspense or wonder or humor. They guide you to creating good entertainment, but not necessarily lasting art.
And like you said, their focus is on mainstream, commercial writing, so that's okay. But there is a certain level of depth that will be missing if you never think about things like theme or meaning. Other writers have covered these topics well, so we know it's not impossible. It's just something that Writing Excuses isn't particularly suited for.
(This could easily become a totally subjective point. In saying that they don't cover how to write with meaning, I'm comparing them to other sources like K.M. Weiland's site. She emphasizes theme above all else, and by comparison, Writing Excuses is rather slack.)