The config defer stuff feels like it's something that should be centrally handled by the module system. i.e. there are other use cases for "please let me run my hook again a bit later", and we could potentially use that to replace hook_module_implements_alter() one day. I'm not necessarily opposed to committing this baked into config to unblock this issue, although I need to think about that a bit more, but can we open a follow-up to discuss factoring it out at least? There too much stuff in here that knows too much about the module system.