It's Windows that does the deleting. No command line processor is involved. That registry location is also used when installers can't update a file that is in use and requires Windows to be rebooted before the install is actually completed.
Notice that the value name is "PendingFileRenameOperations". That's because it's actually used to rename files, and renaming to a "blank" means delete. If you highlight that value in the registry and hit Enter, you'll see that there are multiple lines. The first line is the first file to rename, the second line is what to rename that file to or delete if the line is blank. The third line is the second file to rename or delete, and so on.
Next time you install something and you're told you have to reboot, check out that value and/or run MoveLater to see what I'm talking about.
And lastly, if there are no files set to be renamed or deleted on startup, the value "PendingFileRenameOperations" won't exist at all.