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I'm a little confused how x64 gets away with this. Do they just stubbornly use whatever microcode was on it when the system switched on?

Unfortunately yes. The nonfree channel linked in this thread does/has microcode updates but mainline guix doesn't.

That's just.. so counterproductive. They are ok with proprietary software, but only if they come builtin.

But there are some spectre and meltdown mitigations that comes with CPU microcode, right? It's probably not a great idea to not apply microcode updates in this case

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