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Flatpak sandboxing uses bubblewrap, which uses seccomp and can filter syscalls.
LXD/Incus can run qemu-kvm virtual machines in addition to containers. In fact, I like the security posture of LXD/Incus better here because they use cgroups, namespaces, seccomp, to sandbox the qemu process, which libvirt also does but proxmox does not.
Yes, I understand Flatpak does some seccomp syscall filtering. It still isn't enough to consider a secure sandbox where the threat model is that the app is untrusted. Bubblewrap is generally considered a weak sandbox and isn't "secure by default", allowing for easy footguns.
LXC/Incus does support proper VMs but it isnt as common.
Neither are really designed to run untrusted apps.
~~LXC is namespaces only, maybe you're thinking of libvirt~~ I stand corrected about LXD, never knew it did that, weird I don't know why you'd wanna do that instead of using libvirt.
Flatpack uses namespaces. And unless you have it disabled in the kernel, namespaces can be nested. There's nothing stopping a browser running a flatpack from using namespaces itself.
Not to say that you are incorrect about namespaces vs security. Namespaces are not as secure as a VM.