In my opinion, the main reason for deciding between StandaloneVM and 
Template-based-VM is not security, it is management. With a Template-based-VM, 
you manage all or most of the apps in the template. If you have a single VM 
template for many Template-based-VMs, you just update the template and reboot 
the related VMs that are running. With standalone VMs, you need to update all 
of them separately.

Security concerns:

a. Malware might not survive reboot of Template-based-VM. This is however true 
just for some malware that is not adapted to Qubes OS, ale even this malware 
might survive VM reboot. AFAIR, this is explicitly a non-goal. There are many 
places to hook the malware after reboot – .bashrc, /usr/local/bin, browser 
extensions, …
b. When you have a StandaloneVM you don't run often, it might miss some 
updates, so you are more likely to run some software with known vulnerabilities 
after boot. This does not happen for Temlate-based-VM provided that you use 
some other VMs from the same template.
c. On the other hand, Template-based-VMs always require a reboot after 
updating. Without that, you can still run outdated software with some known 
vulnerabilities.

So, it depends on how you use it.

Regards,
Vít Šesták 'v6ak'

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