Commissioning vs qualification for an IT system

I just started a new job - the master CSV plan here calls for commissioning of the system before qualification. This makes sense to me for a process control system or other system that consists of integrated hardware and software. However, I don’t see where commissioning qualification is appropriate for an IT system where the IT guy buys a software package, installs it, then turns it over to me to validate. In situations like this, I would only qualify the software, assuming the infrastructure was already qualified.

Any opinions? Thanks!