It would be fantastic to not only show the id when entering wlrctl toplevel list
But also to be able to window match on just the id number too so you'd enter wlrctl window focus id:3
I think this would be neat, but it's not easily supported by the protocol. FTM is intended to be used in a continuous way, so the client application can distinguish toplevels by their object ids and there is no issue.
For two different wayland clients (i.e. two invocations of wlrctl), there is no guaranteed event order or persistent uniquely identifying info communicated by the compositor that could be used to make this work. I'll leave this open for now in case I missed something, but I don't know if it even would be a good idea to modify the protocol to support this use case even if that could be easily done.