I know it shouldn't be included in the command line field, but the command that I tested from the command line is:
It IS needed when you run the command from the command line; it is NOT needed when you configure the command line parameters in a package. It's that simple.
So how do I get Patch Manager to yield the same results as running this from the command prompt?
Configure the package correctly.
Remove the /qn and /noreboot, then re-publish, run again, and show us what you get.