The hierarchy file conversion works fine as long as the content Runtime is not in the program files folder but in some location of your convenience where you have full access rights. The generated .cr2 goes into that Runtime folder.

The only files in the installation folder users may want to tamper with are Python scripts in the scriptsmenu. PoserPython offers user-writable storage (PoserTempLocation and PoserPrefsLocation) where scripts can do their storage as appropriate. Older scripts may still rely on free write to subfolders. In that case you could consider changing the permissions to these subfolders or, indeed, install Poser elsewhere.