[dnanian]

The powermanagement.plist is in the "system" area, and as such is isolated from that on your main drive. It should be rebuilt when necessary, but not necessarily on boot: you may have to make changes to the Preference Pane to get a new one written.

The Safety Clone will help to isolate that file, but it won't prevent it from being created... in fact, /Library/Preferences looks, on a Safety Clone, just like a "regular" system's /Library/Preferences. Nothing special.