Virtual Machine on a Commlink, issues.

[Kiirnodel]

Virtual Machine outright says that all it does is let you run two additional programs. If they were locked down, it would say it in the original program (something like: these programs cannot be changed until you reload virtual machine, but it doesn't).

No, instead the drawback is that Virtual Machine leaves your cyberdecks vulnerable to excess matrix damage. By loading virtual machine into a hardwired program carrier, you can't turn it off, so you are always vulnerable.