CRC: "software" hive vs. "system" hive?

The now removed compacter of CRC only compacted the software hive, right? Is there any reason why you left the system hive untouched? Is this also the case with the reg-cleaner? I believe CFP/CIS writes stuff in the system hive, since its size increased heavily after installing CFP/CIS (in my case from about 2 MB to 2.5 MB). Non-purged D+ items in CFP was therefore not found by CRC, right? RegSeeker found those invalid entries.

Thanks for any clarification.