What security risk when using apt / dnf tools to update standalone VM?

What happens if I updated my template VMs using ‘apt update’ and ‘dnf update’ instead of using Qubes OS builtin update tool?

Actually I’ve learned that this method bypasses important security measures provided by Qubes OS, but, I think, for only Dom0 and template VMs not for standalone VMs.

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correct! I never tried to update StandaloneVMs with the Qubes included update procedures.
Always using the update functions of the Standalone builds.

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Do you know of any negative effects of using the Qubes method?
Of course, I have always installed packages the standalone way, but I used the Qubes way of updating them.

Not sure of any negative effects. I’ve always was thinking, in Standalones, you just can update the standalone qube via it’s update functions only and the qubes update functions wouldn’t work here.

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