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The "hide protected operating system files" option only hides files with the Hidden and System attributes set. Hiding all files with the Hidden attribute is easy, though.
In the Folder Format dialog there's a Filter page where you can filter things by attributes and/or names:
Turning on the H checkbox in the Hide Filter section means files with the Hidden attribute will be hidden from view.
To make this change permanent for all folders you should go to Preferences and edit each of your folder formats, as described in the Folder Formats FAQ.