I don't think there were be restrictions - but there will be rules of the road that should be followed otherwise things would break.
I don't see these hooks as being things end users touch in general. It will be the tools that are developed on top of Node-RED that make use of these hooks that will be what end users touch.
So yes, there will be scope for things going wrong, but to some degree it will be up to those tools to manage... we just have to make sure the hooks are well-defined and understood.
Yes... but again, if something is touching the clone flag, it needs to know what it is doing and it needs to be aware that it doesn't exist in isolation. But I don't see there being lots of things wanting to touch the clone flag - especially wanting to set it to true. It's far more likely that something wants to set it to false to prevent any further cloning from happening.
That's an interesting idea. Technically, this proposal would allow that. We need to evaluate if that is a sensible thing to allow, or even if its technically possible, whether its something we'd endorse doing.