Follow-up from "Permanently enables dependency_proxy_read_write_scopes"

The following discussion from !189014 (merged) should be addressed:

• @10io started a discussion:

  This will need a cleanup.

  Basically, we have:

  • this empty file.
  • the EE::VirtualRegistries file that contains logic.

  We need to:

  • Remove the EE override.
  • Update the empty file with the logic from the EE override.
  • Verify that all calls to the logic to don't reference EE::