I eventually did what my father always told me: "When all else fails, dig the manual out of the garbage." I went to the Trash and grabbed the READ ME FIRST.rtf.
The readme for the newest CPU Director includes this pithy statement:
Note: DFS and Power Management functions require Mac OS X 10.3.9 or later, and require a PowerLogix 7447A CPU card. If you purchased a PowerLogix 7447A CPU card prior to July 27, 2005 your card requires CPU Compatibility Updater, which will be sent to existing customers. (If you have a PowerLogix 7447A CPU card and the thermal pane does not appear in CPU Director, or Processor Performance does not appear in the Energy Saver System Preference, you need the CPU Director Compatibility Updater.)
I dutifully emailed Powerlogix support to ask for the CPU Director Compatibility Updater. They sent me the program, I ran it, and System Preferences > Energy Saver > Options > Processor Performance reappeared. The problem is, since this upgrade my machine systematically overheats when I tell it to choose Processor Performance: Automatic. My G4 has not had problems this bad (and subsequently caused kernel panics) since the update to 10.4.3.
The ultimate solution to this problem would be dynamic CPU switching but also failsafe temperature monitoring that allowed CPU Director to force the computer down to the lower speed if overheating becomes imminent. Apparently this exists for some of the Powerlogix CPUs but it sure doesn't show up in my CPU Director software (I have the Powerlogix 7447A).
There has been no word yet from Powerlogix about this issue and I'm going to have to step back in CPU Director versions. Hopefully the CPU Director Compatibility Updater won't make my setup incompatible with previous version of CPU Director. If anyone else has had similar issues and/or has a solution, feel free to post in the comments.