Due the fact that I've found no other solution so far, I've created an initializer which symlinks the ember engine directories of all rails engines into the node_modules of the consuming ember engine in the consuming rails app:
# Get the node_modules dir
nm_dir = Rails.root.join('frontend', 'node_modules')
# Delete existing symlinks
Dir.new(nm_dir.to_s).each { |entry| FileUtils.rm_rf(entry) if entry =~ /^.+\-frontend$/ }
# MODULES contains an array of the rails engine gem names
MODULES.each do |module_name|
  # Each module has a Manifest class, load that
  manifest = load_manifest(module_name)
  # Get the path to the frontend dir of the rails engine
  source = Pathname.new(manifest.method(:setup).source_location[0].split('/lib/')[0]).join('frontend').to_s
  # Symlink destination
  destination = nm_dir.join("#{module_name}-frontend").to_s
  # Symlink it
  FileUtils.symlink source, destination, force: true
end
This approach is probably not very clean, but it seems to work.