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.
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.