It's all a bit theorical though, isn't it? All those user ids aren't necessarily human.
Look at a non-trivial application such as Postfix. It still is simple enough to be understood by one individual human, but it's complex enough to make use of file system rights and various forms of interprocess communication to do its job.
Once you've re-implemented this with unikernels, haven't you re-invented access control and authorization, which you wanted to do without? And yet, you've only got your email transport up. Still a long way to go for a modern collaboration server.
Real world systems, like airline bookings or ERPs, are orders of magnitude more complex than that. I'm not convinced I'd not rather have those use standard components for things like ACLs, process accounting and user ids. They were invented for a reason, and makes it easier to reason about data at rest and things like backups and process scheduling. My suspicion is that you'd want to reinvent them pretty soon when your system grows beyond that single micro service.