Currently, to customize Creo, you dump your custom files in several locations throughout the original files structure, probably with a script because you don't want to forget where they all go, and when you update Creo, they all disappear and you have to do it all over again.
What you should have is a plug-in directory which would contain any customized files placed in an identical directory structure within each plug-in within the plug-in directory.
For example, a custom config.pro would be in Plug-ins\yourpluginnamehere\Common Files\Text\config.pro. It would not be limited. If you included Plug-ins\mynewplugin\Common Files\fakefolder\fakefile.fake, then it would be as if you added fakefolder\fakefile.fake to your Common Files directory. Is this sounding familiar? Then you probably downloaded a mod for a computer game in the last few decades. This is how it's done.
Customizations would be more easily managed, not lost in the soup of original files.
Customzations would not be lost when an update is performed because the plug-ins directory would be left untouched (for better or worse, but that's our job!).