Your own (application and) supervision tree becomes important once you decide to build the application independent of Phoenix - i.e. Phoenix is simply used to build the web interface for your application - an approach advocated in
Discussion: Don’t add a database layer to your Phoenix application
(example)
and demonstrated in
Functional Web Development with Elixir, OTP, and Phoenix (Pragprog).
See also: What do they actually mean when they say "Phoenix is not your application"?