It means phoenix is not the main concern when You start your project. It should be business/domain logic first, and only then, wrap phoenix around.
@pragdave is advocating for this, and in his course, he starts building a game engine, then only after, he wraps it with a web interface. and shows how simple it is to change interface… like a text console interface.
In practice, that means umbrella project are strongly encouraged, as a way to separate concern.
Also, as a personal opinion, I find very nice to build simple domain modules, join them together, and only at the end, add phoenix as web interface 
I think it was a Rails concern at first, where building huge monolithic application was usual.
