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You're also ignoring the amount of work the kernel has to do to shift UUIDs around, the resources that the docker daemon itself uses and amounts of redundant stuff to make sure those processes are running that would usually be handled by systemd on a clean system. Yes, containerization is much better nowadays but still overhead.
Can't comment much about the docker side since it's not something I'm familiar with.
For the kernel part, assuming what you're referring to as UUIDs is the pid namespace mechanism, I'm failing to see how that would add overhead with containers. The namespace lookups/permission checks are performed regardless of whether the process is in a container or not. There is no fast path for non-containerized processes. The worst overhead that this could add is probably one extra ptr chase in the namespace linked list.