Hi,
ThinApp put this isolation mode for system related folders. It is just to avoid accidental modification of system files.
E.g. %SystemSystem% folder contains all system dlls for windows. By making DirectoryIsolationMode=WriteCopy, ThinApp assures that all modifications on this folder by ThinApped application will be reflected in sandbox and native system will remain unaffected.
If you check list given by Lakshman, you will observe that all the folders with ‘WriteCopy’ isolation mode are important folders for application and system working, so its better not to not modify these isolation modes.