The user should not have to finalize the registry cleanup immediately after rebooting. Other registry cleaners allow you to undo changes made to the registry after the fact.
In other words, I can run the registry cleaner, reboot, use my system and even reboot again and still be able to undo changes that the cleaner made to the registry.
After reboot, you can ignore the prompt and finalize any time later. Also, under Settings in CRC, you can restore the changes under the Backup section.