Windows protected folder have more than one function. If a program don't install all files in the correct Windows directory you can have problems. When you put these files in windows protected folder you force window to used and allocate all these files even if they are install in the wrong directory. Controlled folder access applies to a number of system folders and default locations, including folders such as Documents, Pictures, Movies, and Desktop.
You can add additional folders to be protected, but you cannot remove the default folders in the default list.
Adding other folders to Controlled folder access can be useful, for example, if you don't store files in the default Windows libraries or you've changed the location of the libraries away from the defaults