I would use the native version. For something like this, it makes sense that it should have less restricted/sandboxed access to the underlying system.
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virt-manager only requires access to the libvirtd socket, as long as the flatpak.has that as default configuration (which I imagine would be the case), there's zero difference beteween flatpak and native.
Hmm, wouldn't the virt manager just be a frontend and communicate with the virtd socket though?