While I cannot confirm or refute the removal of these point I would point out that such a broad include is likely guaranteed to cause huge system wide issues.
I'm confused. You report this as a bug but it looks like you've put this in the ccleaner.ini file yourself, and if so it's a simple matter of removing it and not using it anymore.
Like Nergal mentioned that can cause system issues, such as the very slow operation of CCleaner, or the removal of a .tmp file which is needed such as during a software install or update. But then again I don't know how effective it could actually be since it isn't using |RECURSE at the end of it.
Are you saying just enabling "Custom Files and Folders" automatically inputs the setting "Include1=PATH|C:\|*.tmp|REMOVESELF" ? I've tried disabling it, restarting CCleaner, enabling it, exiting CCleaner and that entry doesn't appear in the ccleaner.ini file for me.
I don't know if that's what you meant or not, if not please try to explain it differently so we understand exactly.