From a learning perspective you should probably stick to a vanilla configuration because that is what the documentation, blogs, books, videos, etc. assume anyway.
Now if you have a need to use MongoDB you may want to tackle that separately as an Elixir/MongoDB problem which may or may not include include Ecto (example: How to use MongoDB With Elixir - Revisited). With the Phoenix is not your application approach it should be possible to compartmentalize the MongoDB dependency in a distinct application that Phoenix is a client to.
