I wasn't personally working on this, so I apologize for being fuzzy on the details, but I understand that getting rebar3 to fetch all the deps that would normally be managed by hex was not possible or at least non-trivial. There was talk of having to manually install each dep that you knew the Elixir lib would be requiring.
I think it was sorted into something workable, but if anyone has better understanding I would love to be pointed to some resources!
Not a seamless setup, but it does work. As the sibling comment suggests, perhaps using mix for everything would help.
I'll ask around in the company for more information.
I've worked briefly on wrapping an existing erlang app in a Elixir (Nerves) container and I did have a few issues around dependency management which required small changes here and there, but nothing major.
One area where I usually spend more time than I'd like is to get type specifications in good shape so that dialyzer doesn't report too many warnings, but that gets better with every Erlang/Elixir release.