Well, this is my first attempt to implement @hauleth idea. Some kind of composability is still possible

defmodule CustomEctoFrom do
  defmacro __using__(map) do
    quote do
      require Ecto.Query

      defmacro from(expr, kw) do
        kw = CustomEctoFrom.traverse(kw, unquote(map))

        quote do
          Ecto.Query.from(unquote(expr), unquote(kw))
        end
      end
    end
  end

  def traverse({function, args}, map) when is_atom(function) do
    {function, traverse(args, map)}
  end

  def traverse({function, meta, args}, map) do
    function =
      case Map.fetch(map, function) do
        {:ok, aliased_to} -> aliased_to
        :error -> function
      end

    {traverse(function, map), meta, traverse(args, map)}
  end

  def traverse(kw, map) when is_list(kw) do
    for elem <- kw, do: traverse(elem, map)
  end

  def traverse(term, _map), do: term
end

defmodule OtherModuleWithExtensions do
  defmacro concat(a, b) do
    quote do
      fragment("? || ?", unquote(a), unquote(b))
    end
  end
end

defmodule Test do
  import Ecto.Extension.Query.API
  import OtherModuleWithExtensions
  use CustomEctoFrom, %{cond: :cond_, <>: :concat}

  def test do
    from users in "users",
      select: %{
        full_name: users.first_name <> " " <> users.last_name,
        email: users.email,
        role_label:
          cond do
            users.role == "director" -> "DIRECTOR!"
            users.inserted_at < ago(6, "month") -> "OLD!"
            true -> type(users.role, :string)
          end,
        id: users.id
      }
  end
end