I found that Custom Items can be setup in PDQ Inventory however there seems to be no way of setting the value of these custom items from PDQ Deployment packages.
Here is an example use case:
I have a package I deploy to update BIOS settings, PDQ inventory does not pick up these settings during a scan. I would like have have a Final step in the package that changes the Custom Item value. So if my package turns on AUTO POWER ON in the bios my custom item "BiosAutoPowerON" would have its Yes/No value set to YES. This would then limit future deployments to only those computers who need to be changed.