Setting config variables for escript.install

Summary: When running mix escript.install github me/myrepo, configuration options (either defined in config.exs OR in application.env) are not executed. However, if I locally pull down the code and run mix escript.build for the local directory, config.exs is used correctly.

Is this a bug in elixir or am I doing something wrong?

Example code:

config.exs

config :myapp myflag: 42

mix.exs

def application do
  [
    extra_applications: [:logger],
    env: [myflag: 42]
  ]

myapp.ex

def main(args) do
  Application.get_env(:myapp, :myflag)
  |> IO.inspect
end

expected: 42, actual: nil when pulling from github