The super POM contains default folders for resources that are NOT filtered (src/main/resources and src/test/resources). If one (additionally) needs a filtered resources folder, it needs to override the default and therefore has to add all default folders if he does NOT want to "loose" the defaults.
To make this easier my suggestion is to add filtered resource folders to the super POM. This should also fit to the philosophy of maven that aims to have defaults and only declare as little custom configuration as needed.
My personal favorite for the foldernames would be "templates" but to make things more obvious to the user maybe "resources-filtered" would be better. Actually I do not care to much about the name...
So the resources in the super POM should look like this:
Update: The folder name has been changed to "resources-filtered".