I think it would be quite beneficial if when a user removes CCleaner from Add/Remove programs, that the uninstall program moves CCleaner.ini to the User's Desktop so that is the user wants to reinstall later - they can just place their selections back quite easily.
That was one of the files I'd manually backup onto another disk when I still used the install version.
Another possibility is they don't delete it since it's not included by default which is possibly more feasible instead of moving files (well that's the way Inno Setup works by default), that way if re-installing it's right where it needs to be. Unless of course if they started using the ProgramData folder for storing it like most other software does.
The problem is that if you leave things behind following an uninstall (and many apps do) then users complain that it hasn't been completely uninstalled.
Most users want an uninstall to remove everything related to the uninstalled app.
As suggested the best way if you want to keep a copy for possible future use is to make your own backup of your CCleaner.ini file.
I'm always changing settings when answering questions here, so I keep a copy of my CCleaner.ini in my Documents folder so that I can quickly copy/paste it into the CCleaner folder to put my own settings back.